Starting phenix.real_space_refine on Sun Jul 5 20:01:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8y_44362/07_2026/9b8y_44362.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 V 40 8.30 5 S 152 5.16 5 C 19340 2.51 5 N 5232 2.21 5 O 5208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 4, 'ARG:plan': 14, 'ASP:plan': 16, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 228 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'DVT': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 9.46, per 1000 atoms: 0.32 Number of scatterers: 29980 At special positions: 0 Unit cell: (158.148, 158.148, 148.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) V 40 22.97 Ca 8 19.99 S 152 16.00 O 5208 8.00 N 5232 7.00 C 19340 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: 2.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.844A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.555A pdb=" N MET A 581 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 Processing helix chain 'A' and resid 607 through 634 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 644 " --> pdb=" O ARG A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.618A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 906 Processing helix chain 'A' and resid 907 through 913 Processing helix chain 'A' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE A 920 " --> pdb=" O LEU A 916 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 929 " --> pdb=" O LYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1172 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.844A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE B 201 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 503 through 512 Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 581 removed outlier: 3.555A pdb=" N MET B 581 " --> pdb=" O TYR B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 603 Processing helix chain 'B' and resid 607 through 634 Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.617A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 861 Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 906 Processing helix chain 'B' and resid 907 through 913 Processing helix chain 'B' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE B 920 " --> pdb=" O LEU B 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 921 " --> pdb=" O GLY B 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 928 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 929 " --> pdb=" O LYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.929A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1172 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE C 201 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 329 through 337 removed outlier: 3.503A pdb=" N ARG C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 503 through 512 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET C 581 " --> pdb=" O TYR C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 603 Processing helix chain 'C' and resid 607 through 634 Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.795A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 644 " --> pdb=" O ARG C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 removed outlier: 3.619A pdb=" N PHE C 698 " --> pdb=" O VAL C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 906 Processing helix chain 'C' and resid 907 through 913 Processing helix chain 'C' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE C 920 " --> pdb=" O LEU C 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL C 921 " --> pdb=" O GLY C 917 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C 928 " --> pdb=" O SER C 924 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 929 " --> pdb=" O LYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.825A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1053 through 1071 removed outlier: 3.966A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.240A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1172 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.799A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.843A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 177 removed outlier: 3.550A pdb=" N ARG D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.540A pdb=" N ILE D 201 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.798A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 329 through 337 removed outlier: 3.504A pdb=" N ARG D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 4.051A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 425 through 435 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 581 removed outlier: 3.556A pdb=" N MET D 581 " --> pdb=" O TYR D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 603 Processing helix chain 'D' and resid 607 through 634 Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.796A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 644 " --> pdb=" O ARG D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.617A pdb=" N PHE D 698 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 906 Processing helix chain 'D' and resid 907 through 913 Processing helix chain 'D' and resid 916 through 953 removed outlier: 3.792A pdb=" N ILE D 920 " --> pdb=" O LEU D 916 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 921 " --> pdb=" O GLY D 917 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS D 928 " --> pdb=" O SER D 924 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 929 " --> pdb=" O LYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 974 removed outlier: 4.826A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.928A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1053 through 1071 removed outlier: 3.965A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.239A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1172 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.480A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 231 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 119 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.304A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 231 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 119 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 991 removed outlier: 4.305A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TRP B1000 " --> pdb=" O SER B 991 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 231 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 119 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 991 removed outlier: 4.303A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP C1000 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77 removed outlier: 6.479A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 231 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 119 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.139A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 991 removed outlier: 4.304A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP D1000 " --> pdb=" O SER D 991 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.45: 13164 1.45 - 1.67: 17148 1.67 - 1.89: 296 1.89 - 2.11: 112 2.11 - 2.33: 32 Bond restraints: 30752 Sorted by residual: bond pdb=" CB THR B 823 " pdb=" CG2 THR B 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB THR C 823 " pdb=" CG2 THR C 823 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB THR A 823 " pdb=" CG2 THR A 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB THR D 823 " pdb=" CG2 THR D 823 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB TRP A 820 " pdb=" CG TRP A 820 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.46e-01 ... (remaining 30747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 40539 0.98 - 1.96: 1456 1.96 - 2.94: 165 2.94 - 3.92: 116 3.92 - 4.90: 44 Bond angle restraints: 42320 Sorted by residual: angle pdb=" CA TRP C1058 " pdb=" CB TRP C1058 " pdb=" CG TRP C1058 " ideal model delta sigma weight residual 113.60 109.39 4.21 1.90e+00 2.77e-01 4.91e+00 angle pdb=" CA TRP B1058 " pdb=" CB TRP B1058 " pdb=" CG TRP B1058 " ideal model delta sigma weight residual 113.60 109.42 4.18 1.90e+00 2.77e-01 4.84e+00 angle pdb=" CA TRP D1058 " pdb=" CB TRP D1058 " pdb=" CG TRP D1058 " ideal model delta sigma weight residual 113.60 109.43 4.17 1.90e+00 2.77e-01 4.81e+00 angle pdb=" CA TRP A1058 " pdb=" CB TRP A1058 " pdb=" CG TRP A1058 " ideal model delta sigma weight residual 113.60 109.43 4.17 1.90e+00 2.77e-01 4.81e+00 angle pdb=" C PRO C 340 " pdb=" N LYS C 341 " pdb=" CA LYS C 341 " ideal model delta sigma weight residual 121.54 125.59 -4.05 1.91e+00 2.74e-01 4.51e+00 ... (remaining 42315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 16920 15.71 - 31.42: 780 31.42 - 47.13: 204 47.13 - 62.84: 52 62.84 - 78.56: 4 Dihedral angle restraints: 17960 sinusoidal: 6732 harmonic: 11228 Sorted by residual: dihedral pdb=" CA HIS A 447 " pdb=" C HIS A 447 " pdb=" N GLY A 448 " pdb=" CA GLY A 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" CA HIS B 447 " pdb=" C HIS B 447 " pdb=" N GLY B 448 " pdb=" CA GLY B 448 " ideal model delta harmonic sigma weight residual 180.00 164.20 15.80 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CA HIS C 447 " pdb=" C HIS C 447 " pdb=" N GLY C 448 " pdb=" CA GLY C 448 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 ... (remaining 17957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3253 0.029 - 0.058: 1102 0.058 - 0.087: 274 0.087 - 0.116: 118 0.116 - 0.144: 21 Chirality restraints: 4768 Sorted by residual: chirality pdb=" CA ILE D 271 " pdb=" N ILE D 271 " pdb=" C ILE D 271 " pdb=" CB ILE D 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE C 271 " pdb=" N ILE C 271 " pdb=" C ILE C 271 " pdb=" CB ILE C 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 4765 not shown) Planarity restraints: 5232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 456 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO D 457 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 457 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 457 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 456 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 457 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 457 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 457 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 456 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 457 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.026 5.00e-02 4.00e+02 ... (remaining 5229 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 457 2.68 - 3.23: 30832 3.23 - 3.79: 48222 3.79 - 4.34: 59929 4.34 - 4.90: 103139 Nonbonded interactions: 242579 Sorted by model distance: nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.120 3.250 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.120 3.250 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.120 3.250 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.121 3.250 nonbonded pdb=" NH1 ARG D 195 " pdb=" O PRO D 217 " model vdw 2.209 3.120 ... (remaining 242574 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.004 0.041 30752 Z= 0.209 Angle : 0.475 4.903 42320 Z= 0.261 Chirality : 0.034 0.144 4768 Planarity : 0.003 0.046 5232 Dihedral : 10.411 78.556 10696 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.54 % Allowed : 4.62 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.15), residues: 3832 helix: 2.80 (0.11), residues: 2432 sheet: -0.17 (0.39), residues: 200 loop : -0.63 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 442 TYR 0.007 0.001 TYR A1063 PHE 0.013 0.001 PHE B 931 TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (30752) covalent geometry : angle 0.47491 / 0.26 (42320) hydrogen bonds : bond 0.12248 / 8.31 ( 1892) hydrogen bonds : angle 5.01710 / 3.66 ( 5496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 490 time to evaluate : 1.252 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 254 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 332 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8692 (ttm170) REVERT: A 431 ASP cc_start: 0.8518 (t0) cc_final: 0.8207 (t0) REVERT: A 622 MET cc_start: 0.8020 (mtp) cc_final: 0.7782 (mtp) REVERT: B 254 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 332 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8613 (ttm170) REVERT: B 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8227 (t0) REVERT: C 254 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 332 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8592 (ttm170) REVERT: C 431 ASP cc_start: 0.8525 (t0) cc_final: 0.8211 (t0) REVERT: C 1153 GLN cc_start: 0.9281 (pt0) cc_final: 0.9078 (pp30) REVERT: D 254 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 332 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8614 (ttm170) REVERT: D 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8230 (t0) outliers start: 16 outliers final: 0 residues processed: 502 average time/residue: 0.1974 time to fit residues: 156.8008 Evaluate side-chains 329 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 831 GLN A1014 GLN A1017 ASN B 247 ASN B 831 GLN B1014 GLN B1017 ASN C 247 ASN C 831 GLN C1014 GLN C1017 ASN D 247 ASN D 831 GLN D1014 GLN D1017 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.074060 restraints weight = 78239.192| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.20 r_work: 0.2884 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30752 Z= 0.129 Angle : 0.559 8.674 42320 Z= 0.282 Chirality : 0.038 0.236 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.495 15.652 4284 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 8.93 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.14), residues: 3832 helix: 2.68 (0.11), residues: 2424 sheet: 0.11 (0.36), residues: 236 loop : -0.65 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 857 TYR 0.018 0.001 TYR A 103 PHE 0.014 0.001 PHE A 902 TRP 0.010 0.001 TRP A1058 HIS 0.008 0.001 HIS C1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (30752) covalent geometry : angle 0.55945 / 0.28 (42320) hydrogen bonds : bond 0.04186 / 2.85 ( 1892) hydrogen bonds : angle 4.18595 / 3.04 ( 5496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 434 time to evaluate : 1.205 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 430 MET cc_start: 0.8991 (tpt) cc_final: 0.8659 (tpt) REVERT: A 431 ASP cc_start: 0.8767 (t0) cc_final: 0.8249 (t0) REVERT: A 868 ASP cc_start: 0.8228 (m-30) cc_final: 0.7740 (m-30) REVERT: A 1146 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 430 MET cc_start: 0.9021 (tpt) cc_final: 0.8695 (tpt) REVERT: B 431 ASP cc_start: 0.8781 (t0) cc_final: 0.8313 (t0) REVERT: B 670 ASP cc_start: 0.8977 (m-30) cc_final: 0.8300 (m-30) REVERT: B 804 ASP cc_start: 0.8992 (t0) cc_final: 0.8788 (m-30) REVERT: B 868 ASP cc_start: 0.8228 (m-30) cc_final: 0.7742 (m-30) REVERT: B 1146 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8048 (tm-30) REVERT: C 430 MET cc_start: 0.9026 (tpt) cc_final: 0.8697 (tpt) REVERT: C 431 ASP cc_start: 0.8792 (t0) cc_final: 0.8328 (t0) REVERT: C 804 ASP cc_start: 0.8990 (t0) cc_final: 0.8787 (m-30) REVERT: C 868 ASP cc_start: 0.8233 (m-30) cc_final: 0.7748 (m-30) REVERT: C 1146 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 1153 GLN cc_start: 0.9508 (pt0) cc_final: 0.9216 (pp30) REVERT: D 430 MET cc_start: 0.9029 (tpt) cc_final: 0.8705 (tpt) REVERT: D 431 ASP cc_start: 0.8777 (t0) cc_final: 0.8310 (t0) REVERT: D 804 ASP cc_start: 0.8990 (t0) cc_final: 0.8789 (m-30) REVERT: D 868 ASP cc_start: 0.8234 (m-30) cc_final: 0.7747 (m-30) REVERT: D 1146 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8035 (tm-30) outliers start: 61 outliers final: 40 residues processed: 469 average time/residue: 0.1832 time to fit residues: 142.7088 Evaluate side-chains 394 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 354 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 301 optimal weight: 3.9990 chunk 340 optimal weight: 7.9990 chunk 215 optimal weight: 30.0000 chunk 267 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.103349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072286 restraints weight = 78422.156| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.23 r_work: 0.2862 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30752 Z= 0.149 Angle : 0.538 8.372 42320 Z= 0.268 Chirality : 0.037 0.138 4768 Planarity : 0.004 0.064 5232 Dihedral : 3.467 15.910 4284 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.23 % Allowed : 10.53 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.14), residues: 3832 helix: 2.64 (0.11), residues: 2416 sheet: -0.09 (0.35), residues: 260 loop : -0.65 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1147 TYR 0.011 0.001 TYR D1063 PHE 0.011 0.001 PHE B 902 TRP 0.009 0.001 TRP B1124 HIS 0.007 0.001 HIS B1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (30752) covalent geometry : angle 0.53833 / 0.27 (42320) hydrogen bonds : bond 0.04102 / 2.79 ( 1892) hydrogen bonds : angle 4.13685 / 3.00 ( 5496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 379 time to evaluate : 1.211 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 431 ASP cc_start: 0.8806 (t0) cc_final: 0.8363 (t0) REVERT: A 868 ASP cc_start: 0.8342 (m-30) cc_final: 0.7807 (m-30) REVERT: A 941 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 1146 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 1149 LYS cc_start: 0.9036 (tppt) cc_final: 0.8797 (tppt) REVERT: B 431 ASP cc_start: 0.8812 (t0) cc_final: 0.8378 (t0) REVERT: B 804 ASP cc_start: 0.9025 (t0) cc_final: 0.8810 (m-30) REVERT: B 868 ASP cc_start: 0.8344 (m-30) cc_final: 0.8046 (m-30) REVERT: B 869 LEU cc_start: 0.9240 (mt) cc_final: 0.8877 (mt) REVERT: B 941 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9112 (mp) REVERT: B 1146 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8015 (tm-30) REVERT: C 431 ASP cc_start: 0.8822 (t0) cc_final: 0.8385 (t0) REVERT: C 804 ASP cc_start: 0.9007 (t0) cc_final: 0.8793 (m-30) REVERT: C 868 ASP cc_start: 0.8344 (m-30) cc_final: 0.7808 (m-30) REVERT: C 941 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9105 (mp) REVERT: C 1146 GLU cc_start: 0.8635 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 1153 GLN cc_start: 0.9526 (pt0) cc_final: 0.9233 (pp30) REVERT: D 431 ASP cc_start: 0.8803 (t0) cc_final: 0.8371 (t0) REVERT: D 804 ASP cc_start: 0.9019 (t0) cc_final: 0.8802 (m-30) REVERT: D 868 ASP cc_start: 0.8356 (m-30) cc_final: 0.8042 (m-30) REVERT: D 941 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9117 (mp) REVERT: D 1146 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8009 (tm-30) outliers start: 95 outliers final: 60 residues processed: 429 average time/residue: 0.1829 time to fit residues: 130.7340 Evaluate side-chains 418 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 354 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 384 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070534 restraints weight = 78940.959| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.21 r_work: 0.2815 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30752 Z= 0.225 Angle : 0.573 8.320 42320 Z= 0.286 Chirality : 0.038 0.136 4768 Planarity : 0.005 0.059 5232 Dihedral : 3.550 21.224 4284 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.19 % Allowed : 11.62 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3832 helix: 2.55 (0.11), residues: 2420 sheet: -0.35 (0.35), residues: 236 loop : -0.71 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1136 TYR 0.012 0.001 TYR D 971 PHE 0.014 0.001 PHE C 627 TRP 0.010 0.001 TRP B 680 HIS 0.008 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (30752) covalent geometry : angle 0.57333 / 0.29 (42320) hydrogen bonds : bond 0.04377 / 2.98 ( 1892) hydrogen bonds : angle 4.23073 / 3.08 ( 5496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 351 time to evaluate : 1.295 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7658 (tppt) REVERT: A 430 MET cc_start: 0.9076 (tpt) cc_final: 0.8820 (tpt) REVERT: A 431 ASP cc_start: 0.8886 (t0) cc_final: 0.8418 (t0) REVERT: A 699 CYS cc_start: 0.8608 (m) cc_final: 0.7944 (t) REVERT: A 868 ASP cc_start: 0.8378 (m-30) cc_final: 0.8056 (m-30) REVERT: A 941 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9118 (mp) REVERT: A 1146 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8160 (tm-30) REVERT: B 430 MET cc_start: 0.9083 (tpt) cc_final: 0.8781 (tpt) REVERT: B 431 ASP cc_start: 0.8909 (t0) cc_final: 0.8464 (t0) REVERT: B 868 ASP cc_start: 0.8383 (m-30) cc_final: 0.8100 (m-30) REVERT: B 869 LEU cc_start: 0.9244 (mt) cc_final: 0.8870 (mt) REVERT: B 941 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9120 (mp) REVERT: B 1134 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9213 (tt) REVERT: B 1146 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 430 MET cc_start: 0.9084 (tpt) cc_final: 0.8782 (tpt) REVERT: C 431 ASP cc_start: 0.8908 (t0) cc_final: 0.8460 (t0) REVERT: C 699 CYS cc_start: 0.8603 (m) cc_final: 0.7919 (t) REVERT: C 868 ASP cc_start: 0.8385 (m-30) cc_final: 0.8065 (m-30) REVERT: C 941 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9102 (mp) REVERT: C 1146 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 1153 GLN cc_start: 0.9515 (pt0) cc_final: 0.9231 (pp30) REVERT: D 430 MET cc_start: 0.9095 (tpt) cc_final: 0.8789 (tpt) REVERT: D 431 ASP cc_start: 0.8911 (t0) cc_final: 0.8480 (t0) REVERT: D 868 ASP cc_start: 0.8387 (m-30) cc_final: 0.8065 (m-30) REVERT: D 941 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9116 (mp) REVERT: D 1146 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8145 (tm-30) outliers start: 94 outliers final: 64 residues processed: 411 average time/residue: 0.1831 time to fit residues: 124.7981 Evaluate side-chains 401 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 331 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 325 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.102897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071780 restraints weight = 78277.027| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.23 r_work: 0.2851 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30752 Z= 0.131 Angle : 0.521 8.809 42320 Z= 0.260 Chirality : 0.036 0.124 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.509 20.365 4284 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.19 % Allowed : 12.40 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.14), residues: 3832 helix: 2.56 (0.11), residues: 2444 sheet: -0.37 (0.35), residues: 236 loop : -0.72 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1136 TYR 0.013 0.001 TYR D 971 PHE 0.014 0.001 PHE D 627 TRP 0.010 0.001 TRP D1058 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (30752) covalent geometry : angle 0.52065 / 0.26 (42320) hydrogen bonds : bond 0.03983 / 2.70 ( 1892) hydrogen bonds : angle 4.06924 / 2.95 ( 5496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 356 time to evaluate : 1.211 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7676 (tppt) REVERT: A 431 ASP cc_start: 0.8888 (t0) cc_final: 0.8413 (t0) REVERT: A 804 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: A 868 ASP cc_start: 0.8409 (m-30) cc_final: 0.8059 (m-30) REVERT: A 941 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9119 (mp) REVERT: A 1146 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 332 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8612 (ttm170) REVERT: B 430 MET cc_start: 0.9076 (tpt) cc_final: 0.8813 (tpt) REVERT: B 431 ASP cc_start: 0.8891 (t0) cc_final: 0.8433 (t0) REVERT: B 868 ASP cc_start: 0.8437 (m-30) cc_final: 0.8083 (m-30) REVERT: B 941 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9118 (mp) REVERT: B 1146 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8163 (tm-30) REVERT: B 1149 LYS cc_start: 0.9081 (tppt) cc_final: 0.8533 (tppt) REVERT: C 332 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8601 (ttm170) REVERT: C 430 MET cc_start: 0.9073 (tpt) cc_final: 0.8800 (tpt) REVERT: C 431 ASP cc_start: 0.8911 (t0) cc_final: 0.8438 (t0) REVERT: C 868 ASP cc_start: 0.8418 (m-30) cc_final: 0.8069 (m-30) REVERT: C 941 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9120 (mp) REVERT: C 1146 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 1153 GLN cc_start: 0.9502 (pt0) cc_final: 0.9225 (pp30) REVERT: D 332 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8620 (ttm170) REVERT: D 430 MET cc_start: 0.9068 (tpt) cc_final: 0.8840 (tpt) REVERT: D 431 ASP cc_start: 0.8881 (t0) cc_final: 0.8421 (t0) REVERT: D 644 ARG cc_start: 0.5837 (tpt170) cc_final: 0.3467 (mmm-85) REVERT: D 868 ASP cc_start: 0.8446 (m-30) cc_final: 0.8091 (m-30) REVERT: D 941 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9111 (mp) REVERT: D 1146 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8101 (tm-30) outliers start: 94 outliers final: 70 residues processed: 414 average time/residue: 0.1811 time to fit residues: 124.2781 Evaluate side-chains 425 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 346 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 332 ARG Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 306 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 325 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.101781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.070534 restraints weight = 78810.051| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.23 r_work: 0.2825 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30752 Z= 0.196 Angle : 0.558 8.631 42320 Z= 0.276 Chirality : 0.037 0.131 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.514 21.956 4284 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.36 % Allowed : 12.87 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.14), residues: 3832 helix: 2.60 (0.11), residues: 2424 sheet: -0.44 (0.34), residues: 236 loop : -0.73 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 459 TYR 0.013 0.001 TYR D 971 PHE 0.012 0.001 PHE D 627 TRP 0.010 0.001 TRP C 680 HIS 0.007 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (30752) covalent geometry : angle 0.55752 / 0.28 (42320) hydrogen bonds : bond 0.04153 / 2.82 ( 1892) hydrogen bonds : angle 4.11248 / 2.98 ( 5496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 339 time to evaluate : 1.164 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7681 (tppt) REVERT: A 431 ASP cc_start: 0.8863 (t0) cc_final: 0.8323 (t0) REVERT: A 699 CYS cc_start: 0.8585 (m) cc_final: 0.7900 (t) REVERT: A 868 ASP cc_start: 0.8458 (m-30) cc_final: 0.7771 (m-30) REVERT: A 941 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9126 (mp) REVERT: A 1146 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 332 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (ttm170) REVERT: B 431 ASP cc_start: 0.8937 (t0) cc_final: 0.8499 (t0) REVERT: B 644 ARG cc_start: 0.5966 (tpt170) cc_final: 0.2683 (tmm160) REVERT: B 699 CYS cc_start: 0.8585 (m) cc_final: 0.7889 (t) REVERT: B 868 ASP cc_start: 0.8443 (m-30) cc_final: 0.7752 (m-30) REVERT: B 941 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9132 (mp) REVERT: B 1146 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 332 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8531 (ttm170) REVERT: C 431 ASP cc_start: 0.8950 (t0) cc_final: 0.8495 (t0) REVERT: C 644 ARG cc_start: 0.5907 (tpt170) cc_final: 0.2629 (tmm160) REVERT: C 699 CYS cc_start: 0.8574 (m) cc_final: 0.7879 (t) REVERT: C 868 ASP cc_start: 0.8467 (m-30) cc_final: 0.7778 (m-30) REVERT: C 941 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9145 (mp) REVERT: C 1146 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8145 (tm-30) REVERT: C 1149 LYS cc_start: 0.9151 (tppt) cc_final: 0.8544 (tppt) REVERT: C 1153 GLN cc_start: 0.9496 (pt0) cc_final: 0.9239 (pp30) REVERT: D 332 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8541 (ttm170) REVERT: D 431 ASP cc_start: 0.8936 (t0) cc_final: 0.8490 (t0) REVERT: D 644 ARG cc_start: 0.5930 (tpt170) cc_final: 0.2642 (tmm160) REVERT: D 699 CYS cc_start: 0.8590 (m) cc_final: 0.7903 (t) REVERT: D 868 ASP cc_start: 0.8461 (m-30) cc_final: 0.7773 (m-30) REVERT: D 941 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9149 (mp) REVERT: D 1146 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8104 (tm-30) outliers start: 99 outliers final: 77 residues processed: 404 average time/residue: 0.1663 time to fit residues: 112.0118 Evaluate side-chains 414 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 329 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 332 ARG Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 78 optimal weight: 2.9990 chunk 369 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 68 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 281 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.072954 restraints weight = 78545.340| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.23 r_work: 0.2870 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30752 Z= 0.110 Angle : 0.525 8.917 42320 Z= 0.261 Chirality : 0.036 0.248 4768 Planarity : 0.004 0.051 5232 Dihedral : 3.469 20.529 4284 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.12 % Allowed : 14.10 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.14), residues: 3832 helix: 2.55 (0.11), residues: 2452 sheet: -0.36 (0.35), residues: 236 loop : -0.70 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 108 TYR 0.012 0.001 TYR A1063 PHE 0.013 0.001 PHE D 627 TRP 0.011 0.001 TRP D1058 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (30752) covalent geometry : angle 0.52534 / 0.26 (42320) hydrogen bonds : bond 0.03821 / 2.59 ( 1892) hydrogen bonds : angle 3.99784 / 2.89 ( 5496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 377 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7655 (tppt) REVERT: A 431 ASP cc_start: 0.8736 (t0) cc_final: 0.8226 (t0) REVERT: A 868 ASP cc_start: 0.8389 (m-30) cc_final: 0.7706 (m-30) REVERT: A 941 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9099 (mp) REVERT: A 1140 LYS cc_start: 0.9268 (tmtt) cc_final: 0.9027 (tmtt) REVERT: A 1146 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 332 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8569 (ttm170) REVERT: B 430 MET cc_start: 0.9093 (tpt) cc_final: 0.8824 (tpp) REVERT: B 431 ASP cc_start: 0.8824 (t0) cc_final: 0.8286 (t0) REVERT: B 644 ARG cc_start: 0.5862 (tpt170) cc_final: 0.3394 (mmm-85) REVERT: B 868 ASP cc_start: 0.8374 (m-30) cc_final: 0.7689 (m-30) REVERT: B 941 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9097 (mp) REVERT: B 1146 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8178 (tm-30) REVERT: C 430 MET cc_start: 0.9106 (tpt) cc_final: 0.8838 (tpp) REVERT: C 431 ASP cc_start: 0.8836 (t0) cc_final: 0.8302 (t0) REVERT: C 644 ARG cc_start: 0.5816 (tpt170) cc_final: 0.3402 (mmm-85) REVERT: C 868 ASP cc_start: 0.8394 (m-30) cc_final: 0.7712 (m-30) REVERT: C 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9101 (mp) REVERT: C 1140 LYS cc_start: 0.9280 (tmtt) cc_final: 0.9061 (tmtt) REVERT: C 1146 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 1153 GLN cc_start: 0.9491 (pt0) cc_final: 0.9232 (pp30) REVERT: D 332 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8582 (ttm170) REVERT: D 430 MET cc_start: 0.9100 (tpt) cc_final: 0.8827 (tpp) REVERT: D 431 ASP cc_start: 0.8822 (t0) cc_final: 0.8282 (t0) REVERT: D 644 ARG cc_start: 0.5832 (tpt170) cc_final: 0.3416 (mmm-85) REVERT: D 868 ASP cc_start: 0.8391 (m-30) cc_final: 0.7705 (m-30) REVERT: D 941 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9098 (mp) REVERT: D 1146 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 92 outliers final: 76 residues processed: 433 average time/residue: 0.1657 time to fit residues: 119.9738 Evaluate side-chains 430 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 347 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 332 ARG Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 332 ARG Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 269 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 372 optimal weight: 0.0170 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.071697 restraints weight = 78634.593| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.25 r_work: 0.2852 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 30752 Z= 0.144 Angle : 0.533 8.335 42320 Z= 0.266 Chirality : 0.037 0.243 4768 Planarity : 0.004 0.050 5232 Dihedral : 3.456 20.713 4284 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.85 % Allowed : 14.13 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2456 sheet: -0.34 (0.35), residues: 236 loop : -0.66 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1136 TYR 0.012 0.001 TYR D 971 PHE 0.013 0.001 PHE B 627 TRP 0.010 0.001 TRP D1058 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (30752) covalent geometry : angle 0.53272 / 0.27 (42320) hydrogen bonds : bond 0.03899 / 2.65 ( 1892) hydrogen bonds : angle 4.00840 / 2.90 ( 5496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 349 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7668 (tppt) REVERT: A 431 ASP cc_start: 0.8825 (t0) cc_final: 0.8218 (t0) REVERT: A 644 ARG cc_start: 0.5925 (tpt170) cc_final: 0.2584 (tmm160) REVERT: A 699 CYS cc_start: 0.8534 (m) cc_final: 0.7820 (t) REVERT: A 868 ASP cc_start: 0.8413 (m-30) cc_final: 0.7738 (m-30) REVERT: A 941 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 1146 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 430 MET cc_start: 0.9071 (tpt) cc_final: 0.8842 (tpp) REVERT: B 431 ASP cc_start: 0.8853 (t0) cc_final: 0.8298 (t0) REVERT: B 644 ARG cc_start: 0.5929 (tpt170) cc_final: 0.3475 (mmm-85) REVERT: B 699 CYS cc_start: 0.8544 (m) cc_final: 0.7821 (t) REVERT: B 868 ASP cc_start: 0.8403 (m-30) cc_final: 0.7732 (m-30) REVERT: B 941 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9132 (mp) REVERT: B 1140 LYS cc_start: 0.9293 (tmtt) cc_final: 0.9065 (tmtt) REVERT: B 1146 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8107 (tm-30) REVERT: C 430 MET cc_start: 0.9089 (tpt) cc_final: 0.8864 (tpp) REVERT: C 431 ASP cc_start: 0.8880 (t0) cc_final: 0.8326 (t0) REVERT: C 644 ARG cc_start: 0.5892 (tpt170) cc_final: 0.3456 (mmm-85) REVERT: C 868 ASP cc_start: 0.8427 (m-30) cc_final: 0.7755 (m-30) REVERT: C 941 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9133 (mp) REVERT: C 1140 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9084 (tmtt) REVERT: C 1146 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 1153 GLN cc_start: 0.9496 (pt0) cc_final: 0.9240 (pp30) REVERT: D 430 MET cc_start: 0.9076 (tpt) cc_final: 0.8841 (tpp) REVERT: D 431 ASP cc_start: 0.8849 (t0) cc_final: 0.8289 (t0) REVERT: D 644 ARG cc_start: 0.5917 (tpt170) cc_final: 0.3485 (mmm-85) REVERT: D 699 CYS cc_start: 0.8542 (m) cc_final: 0.7832 (t) REVERT: D 868 ASP cc_start: 0.8415 (m-30) cc_final: 0.7740 (m-30) REVERT: D 941 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9129 (mp) REVERT: D 1146 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8233 (tm-30) outliers start: 84 outliers final: 74 residues processed: 401 average time/residue: 0.1594 time to fit residues: 106.1976 Evaluate side-chains 419 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 340 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 75 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 350 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 363 optimal weight: 1.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071758 restraints weight = 79126.238| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.27 r_work: 0.2840 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30752 Z= 0.155 Angle : 0.543 8.666 42320 Z= 0.271 Chirality : 0.037 0.256 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.442 20.445 4284 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.82 % Allowed : 14.40 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.14), residues: 3832 helix: 2.52 (0.11), residues: 2456 sheet: -0.39 (0.35), residues: 236 loop : -0.64 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1136 TYR 0.012 0.001 TYR B 971 PHE 0.012 0.001 PHE C 627 TRP 0.010 0.001 TRP C1058 HIS 0.006 0.001 HIS D1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (30752) covalent geometry : angle 0.54259 / 0.27 (42320) hydrogen bonds : bond 0.03934 / 2.67 ( 1892) hydrogen bonds : angle 4.01423 / 2.90 ( 5496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7669 (tppt) REVERT: A 431 ASP cc_start: 0.8836 (t0) cc_final: 0.8359 (t0) REVERT: A 644 ARG cc_start: 0.5915 (tpt170) cc_final: 0.2589 (tmm160) REVERT: A 868 ASP cc_start: 0.8394 (m-30) cc_final: 0.7700 (m-30) REVERT: A 941 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9089 (mp) REVERT: A 1146 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 430 MET cc_start: 0.9124 (tpt) cc_final: 0.8889 (tpp) REVERT: B 431 ASP cc_start: 0.8865 (t0) cc_final: 0.8317 (t0) REVERT: B 644 ARG cc_start: 0.5930 (tpt170) cc_final: 0.2578 (tmm160) REVERT: B 868 ASP cc_start: 0.8393 (m-30) cc_final: 0.7698 (m-30) REVERT: B 929 ASP cc_start: 0.9069 (m-30) cc_final: 0.8846 (m-30) REVERT: B 941 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9093 (mp) REVERT: B 1146 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8186 (tm-30) REVERT: C 430 MET cc_start: 0.9109 (tpt) cc_final: 0.8900 (tpp) REVERT: C 431 ASP cc_start: 0.8877 (t0) cc_final: 0.8336 (t0) REVERT: C 644 ARG cc_start: 0.5904 (tpt170) cc_final: 0.3501 (mmm-85) REVERT: C 699 CYS cc_start: 0.8497 (m) cc_final: 0.7784 (t) REVERT: C 868 ASP cc_start: 0.8403 (m-30) cc_final: 0.7711 (m-30) REVERT: C 929 ASP cc_start: 0.9067 (m-30) cc_final: 0.8812 (m-30) REVERT: C 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 1140 LYS cc_start: 0.9298 (tmtt) cc_final: 0.9061 (tmtt) REVERT: C 1146 GLU cc_start: 0.8698 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 1153 GLN cc_start: 0.9477 (pt0) cc_final: 0.9229 (pp30) REVERT: D 430 MET cc_start: 0.9121 (tpt) cc_final: 0.8913 (tpp) REVERT: D 431 ASP cc_start: 0.8874 (t0) cc_final: 0.8329 (t0) REVERT: D 644 ARG cc_start: 0.5902 (tpt170) cc_final: 0.3516 (mmm-85) REVERT: D 868 ASP cc_start: 0.8408 (m-30) cc_final: 0.7716 (m-30) REVERT: D 941 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9121 (mp) REVERT: D 1140 LYS cc_start: 0.9272 (tmtt) cc_final: 0.9058 (tmtt) REVERT: D 1146 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8140 (tm-30) outliers start: 83 outliers final: 78 residues processed: 398 average time/residue: 0.1607 time to fit residues: 106.4677 Evaluate side-chains 424 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 341 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 36 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 358 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 360 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070478 restraints weight = 79049.192| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.25 r_work: 0.2816 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 30752 Z= 0.201 Angle : 0.572 8.204 42320 Z= 0.287 Chirality : 0.038 0.214 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.485 20.895 4284 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.85 % Allowed : 14.47 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.14), residues: 3832 helix: 2.48 (0.11), residues: 2456 sheet: -0.49 (0.35), residues: 236 loop : -0.61 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 108 TYR 0.013 0.001 TYR D 971 PHE 0.013 0.001 PHE C 627 TRP 0.010 0.001 TRP C1058 HIS 0.006 0.001 HIS D1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (30752) covalent geometry : angle 0.57218 / 0.29 (42320) hydrogen bonds : bond 0.04189 / 2.84 ( 1892) hydrogen bonds : angle 4.09760 / 2.97 ( 5496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7688 (tppt) REVERT: A 431 ASP cc_start: 0.8866 (t0) cc_final: 0.8432 (t0) REVERT: A 644 ARG cc_start: 0.5833 (tpt170) cc_final: 0.2689 (ttp80) REVERT: A 868 ASP cc_start: 0.8446 (m-30) cc_final: 0.7752 (m-30) REVERT: A 941 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9097 (mp) REVERT: A 1146 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 430 MET cc_start: 0.9089 (tpt) cc_final: 0.8886 (tpp) REVERT: B 431 ASP cc_start: 0.8888 (t0) cc_final: 0.8342 (t0) REVERT: B 644 ARG cc_start: 0.5848 (tpt170) cc_final: 0.2687 (ttp80) REVERT: B 868 ASP cc_start: 0.8434 (m-30) cc_final: 0.7741 (m-30) REVERT: B 941 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9096 (mp) REVERT: B 1146 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 430 MET cc_start: 0.9076 (tpt) cc_final: 0.8862 (tpp) REVERT: C 431 ASP cc_start: 0.8891 (t0) cc_final: 0.8354 (t0) REVERT: C 644 ARG cc_start: 0.5796 (tpt170) cc_final: 0.2647 (ttp80) REVERT: C 868 ASP cc_start: 0.8454 (m-30) cc_final: 0.7759 (m-30) REVERT: C 941 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9114 (mp) REVERT: C 1146 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 1153 GLN cc_start: 0.9489 (pt0) cc_final: 0.9242 (pp30) REVERT: D 430 MET cc_start: 0.9084 (tpt) cc_final: 0.8882 (tpp) REVERT: D 431 ASP cc_start: 0.8884 (t0) cc_final: 0.8336 (t0) REVERT: D 644 ARG cc_start: 0.5779 (tpt170) cc_final: 0.2644 (ttp80) REVERT: D 868 ASP cc_start: 0.8453 (m-30) cc_final: 0.7760 (m-30) REVERT: D 941 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9094 (mp) REVERT: D 1146 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8194 (tm-30) outliers start: 84 outliers final: 75 residues processed: 391 average time/residue: 0.1647 time to fit residues: 107.0245 Evaluate side-chains 408 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 328 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 217 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 378 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.070714 restraints weight = 79602.533| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.27 r_work: 0.2821 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30752 Z= 0.177 Angle : 0.562 8.595 42320 Z= 0.280 Chirality : 0.038 0.211 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.483 20.502 4284 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.75 % Allowed : 14.91 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.14), residues: 3832 helix: 2.46 (0.11), residues: 2456 sheet: -0.47 (0.35), residues: 236 loop : -0.58 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1136 TYR 0.013 0.001 TYR B 971 PHE 0.013 0.001 PHE C 627 TRP 0.010 0.001 TRP C1058 HIS 0.006 0.001 HIS D1128 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (30752) covalent geometry : angle 0.56198 / 0.28 (42320) hydrogen bonds : bond 0.04105 / 2.79 ( 1892) hydrogen bonds : angle 4.07807 / 2.95 ( 5496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6836.10 seconds wall clock time: 117 minutes 47.48 seconds (7067.48 seconds total)