Starting phenix.real_space_refine on Tue May 27 23:50:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8y_44362/05_2025/9b8y_44362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8y_44362/05_2025/9b8y_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_44362/05_2025/9b8y_44362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8y_44362/05_2025/9b8y_44362.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8y_44362/05_2025/9b8y_44362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8y_44362/05_2025/9b8y_44362.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B, D Time building chain proxies: 20.73, per 1000 atoms: 0.69 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: 8.76 Conformation dependent library (CDL) restraints added in 3.6 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: 3.68 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: 12.43 Time building geometry restraints manager: 9.82 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 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.120 2.510 nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.120 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.121 2.510 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 69.990 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 PHE 0.013 0.001 PHE B 931 TYR 0.007 0.001 TYR A1063 ARG 0.002 0.000 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.12248 ( 1892) hydrogen bonds : angle 5.01710 ( 5496) covalent geometry : bond 0.00442 (30752) covalent geometry : angle 0.47491 (42320) *********************** 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 : 3.205 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 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: 0.8526 (t0) cc_final: 0.8211 (t0) REVERT: C 1153 GLN cc_start: 0.9281 (pt0) cc_final: 0.9079 (pp30) REVERT: D 254 GLU cc_start: 0.8070 (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: 0.4350 time to fit residues: 341.5387 Evaluate side-chains 330 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN A1017 ASN B 247 ASN B1014 GLN B1017 ASN C 247 ASN C1014 GLN C1017 ASN D 247 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070544 restraints weight = 79221.025| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.20 r_work: 0.2809 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 30752 Z= 0.265 Angle : 0.619 7.427 42320 Z= 0.313 Chirality : 0.040 0.196 4768 Planarity : 0.005 0.047 5232 Dihedral : 3.569 16.269 4284 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.28 % Allowed : 9.51 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3832 helix: 2.47 (0.11), residues: 2452 sheet: 0.15 (0.36), residues: 228 loop : -0.67 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 680 HIS 0.009 0.001 HIS C1128 PHE 0.014 0.001 PHE A 931 TYR 0.016 0.002 TYR A 103 ARG 0.007 0.001 ARG C 857 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 1892) hydrogen bonds : angle 4.43522 ( 5496) covalent geometry : bond 0.00611 (30752) covalent geometry : angle 0.61924 (42320) *********************** 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 420 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 3.676 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 254 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 430 MET cc_start: 0.9021 (tpt) cc_final: 0.8781 (tpp) REVERT: A 431 ASP cc_start: 0.8852 (t0) cc_final: 0.8401 (t0) REVERT: A 699 CYS cc_start: 0.8412 (m) cc_final: 0.8187 (t) REVERT: A 868 ASP cc_start: 0.8320 (m-30) cc_final: 0.8059 (m-30) REVERT: A 1146 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 254 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 430 MET cc_start: 0.9037 (tpt) cc_final: 0.8799 (tpp) REVERT: B 431 ASP cc_start: 0.8863 (t0) cc_final: 0.8419 (t0) REVERT: B 670 ASP cc_start: 0.8998 (m-30) cc_final: 0.8516 (m-30) REVERT: B 699 CYS cc_start: 0.8410 (m) cc_final: 0.8181 (t) REVERT: B 868 ASP cc_start: 0.8348 (m-30) cc_final: 0.8085 (m-30) REVERT: B 1146 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8160 (tm-30) REVERT: C 254 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 430 MET cc_start: 0.9024 (tpt) cc_final: 0.8784 (tpp) REVERT: C 431 ASP cc_start: 0.8880 (t0) cc_final: 0.8437 (t0) REVERT: C 699 CYS cc_start: 0.8391 (m) cc_final: 0.8155 (t) REVERT: C 868 ASP cc_start: 0.8318 (m-30) cc_final: 0.8060 (m-30) REVERT: C 1146 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 1153 GLN cc_start: 0.9536 (pt0) cc_final: 0.9252 (pp30) REVERT: D 430 MET cc_start: 0.9052 (tpt) cc_final: 0.8805 (tpp) REVERT: D 431 ASP cc_start: 0.8868 (t0) cc_final: 0.8427 (t0) REVERT: D 699 CYS cc_start: 0.8402 (m) cc_final: 0.8174 (t) REVERT: D 868 ASP cc_start: 0.8345 (m-30) cc_final: 0.8083 (m-30) REVERT: D 1146 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8147 (tm-30) outliers start: 67 outliers final: 35 residues processed: 388 average time/residue: 0.3941 time to fit residues: 250.0425 Evaluate side-chains 349 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 3.278 ------------------------------------------------------------------------------- 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 434 LEU 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 434 LEU Chi-restraints excluded: chain B residue 648 LEU 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 434 LEU Chi-restraints excluded: chain C residue 648 LEU 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 309 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 858 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 12 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 381 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 340 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.072718 restraints weight = 78779.726| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.24 r_work: 0.2859 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30752 Z= 0.128 Angle : 0.527 9.151 42320 Z= 0.264 Chirality : 0.037 0.199 4768 Planarity : 0.004 0.050 5232 Dihedral : 3.521 16.203 4284 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.09 % Allowed : 10.60 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.14), residues: 3832 helix: 2.61 (0.11), residues: 2424 sheet: 0.00 (0.36), residues: 236 loop : -0.65 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.007 0.001 HIS D1128 PHE 0.009 0.001 PHE C 931 TYR 0.012 0.001 TYR D1063 ARG 0.003 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 1892) hydrogen bonds : angle 4.12052 ( 5496) covalent geometry : bond 0.00281 (30752) covalent geometry : angle 0.52731 (42320) *********************** 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 490 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 399 time to evaluate : 3.186 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 revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.8027 (m) cc_final: 0.7250 (p) REVERT: A 431 ASP cc_start: 0.8798 (t0) cc_final: 0.8376 (t0) REVERT: A 868 ASP cc_start: 0.8372 (m-30) cc_final: 0.8048 (m-30) REVERT: A 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9109 (mp) REVERT: A 1146 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8383 (tm-30) REVERT: B 254 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7781 (mt-10) REVERT: B 431 ASP cc_start: 0.8831 (t0) cc_final: 0.8420 (t0) REVERT: B 868 ASP cc_start: 0.8368 (m-30) cc_final: 0.8046 (m-30) REVERT: B 941 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9103 (mp) REVERT: B 1146 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 254 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 431 ASP cc_start: 0.8841 (t0) cc_final: 0.8429 (t0) REVERT: C 868 ASP cc_start: 0.8378 (m-30) cc_final: 0.8060 (m-30) REVERT: C 941 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9108 (mp) REVERT: C 1146 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8175 (tm-30) REVERT: C 1153 GLN cc_start: 0.9524 (pt0) cc_final: 0.9241 (pp30) REVERT: D 431 ASP cc_start: 0.8829 (t0) cc_final: 0.8418 (t0) REVERT: D 868 ASP cc_start: 0.8379 (m-30) cc_final: 0.8056 (m-30) REVERT: D 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9107 (mp) REVERT: D 1146 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8182 (tm-30) outliers start: 91 outliers final: 59 residues processed: 450 average time/residue: 0.3784 time to fit residues: 279.8763 Evaluate side-chains 415 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 4.136 ------------------------------------------------------------------------------- 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 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 509 MET 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 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 B residue 105 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 509 MET 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 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 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 509 MET 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 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 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 509 MET 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 134 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 379 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 325 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 274 optimal weight: 0.0270 chunk 213 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 overall best weight: 3.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.069882 restraints weight = 79351.176| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.27 r_work: 0.2813 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30752 Z= 0.220 Angle : 0.568 7.789 42320 Z= 0.285 Chirality : 0.038 0.133 4768 Planarity : 0.004 0.055 5232 Dihedral : 3.573 21.397 4284 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.36 % Allowed : 12.26 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2424 sheet: -0.38 (0.34), residues: 236 loop : -0.70 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.007 0.001 HIS A1128 PHE 0.013 0.001 PHE D 627 TYR 0.011 0.001 TYR C 971 ARG 0.009 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1892) hydrogen bonds : angle 4.23126 ( 5496) covalent geometry : bond 0.00508 (30752) covalent geometry : angle 0.56844 (42320) *********************** 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 439 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 340 time to evaluate : 3.094 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 430 MET cc_start: 0.9073 (tpt) cc_final: 0.8780 (tpt) REVERT: A 431 ASP cc_start: 0.8873 (t0) cc_final: 0.8423 (t0) REVERT: A 699 CYS cc_start: 0.8640 (m) cc_final: 0.7975 (t) REVERT: A 868 ASP cc_start: 0.8429 (m-30) cc_final: 0.8106 (m-30) REVERT: A 941 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9139 (mp) REVERT: A 1146 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 430 MET cc_start: 0.9083 (tpt) cc_final: 0.8792 (tpt) REVERT: B 431 ASP cc_start: 0.8887 (t0) cc_final: 0.8451 (t0) REVERT: B 699 CYS cc_start: 0.8634 (m) cc_final: 0.7961 (t) REVERT: B 868 ASP cc_start: 0.8425 (m-30) cc_final: 0.8101 (m-30) REVERT: B 941 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9120 (mp) REVERT: B 1146 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8176 (tm-30) REVERT: C 430 MET cc_start: 0.9071 (tpt) cc_final: 0.8788 (tpt) REVERT: C 431 ASP cc_start: 0.8907 (t0) cc_final: 0.8491 (t0) REVERT: C 699 CYS cc_start: 0.8626 (m) cc_final: 0.7962 (t) REVERT: C 868 ASP cc_start: 0.8435 (m-30) cc_final: 0.8112 (m-30) REVERT: C 941 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9131 (mp) REVERT: C 1146 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 1153 GLN cc_start: 0.9513 (pt0) cc_final: 0.9240 (pp30) REVERT: D 430 MET cc_start: 0.9081 (tpt) cc_final: 0.8791 (tpt) REVERT: D 431 ASP cc_start: 0.8895 (t0) cc_final: 0.8463 (t0) REVERT: D 699 CYS cc_start: 0.8635 (m) cc_final: 0.7975 (t) REVERT: D 868 ASP cc_start: 0.8420 (m-30) cc_final: 0.8096 (m-30) REVERT: D 941 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9123 (mp) REVERT: D 1146 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8199 (tm-30) outliers start: 99 outliers final: 71 residues processed: 407 average time/residue: 0.3988 time to fit residues: 268.9550 Evaluate side-chains 403 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 328 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 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 434 LEU Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 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 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 941 LEU 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 288 ILE 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 440 PHE Chi-restraints excluded: chain B residue 509 MET 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 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 125 SER 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 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 509 MET 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 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 D residue 105 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 155 THR 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 434 LEU Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 509 MET 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 941 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 319 optimal weight: 20.0000 chunk 260 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 233 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 1 optimal weight: 40.0000 chunk 45 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.071510 restraints weight = 78234.511| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.23 r_work: 0.2848 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30752 Z= 0.126 Angle : 0.526 9.064 42320 Z= 0.260 Chirality : 0.036 0.133 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.526 21.150 4284 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.02 % Allowed : 13.18 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3832 helix: 2.54 (0.11), residues: 2444 sheet: -0.36 (0.34), residues: 236 loop : -0.74 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1058 HIS 0.006 0.001 HIS A1128 PHE 0.011 0.001 PHE C 627 TYR 0.012 0.001 TYR D1063 ARG 0.006 0.000 ARG B1136 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 1892) hydrogen bonds : angle 4.09507 ( 5496) covalent geometry : bond 0.00283 (30752) covalent geometry : angle 0.52592 (42320) *********************** 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 453 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 364 time to evaluate : 3.557 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 86 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7657 (tppt) REVERT: A 332 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8655 (ttp80) REVERT: A 430 MET cc_start: 0.9066 (tpt) cc_final: 0.8794 (tpt) REVERT: A 431 ASP cc_start: 0.8855 (t0) cc_final: 0.8387 (t0) REVERT: A 868 ASP cc_start: 0.8426 (m-30) cc_final: 0.8075 (m-30) REVERT: A 941 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 1146 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8272 (tm-30) REVERT: B 86 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7675 (tppt) REVERT: B 430 MET cc_start: 0.9094 (tpt) cc_final: 0.8789 (tpt) REVERT: B 431 ASP cc_start: 0.8872 (t0) cc_final: 0.8404 (t0) REVERT: B 868 ASP cc_start: 0.8420 (m-30) cc_final: 0.8070 (m-30) REVERT: B 941 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9130 (mp) REVERT: B 1146 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 1149 LYS cc_start: 0.9125 (tppt) cc_final: 0.8422 (tppt) REVERT: C 430 MET cc_start: 0.9081 (tpt) cc_final: 0.8731 (tpt) REVERT: C 431 ASP cc_start: 0.8887 (t0) cc_final: 0.8424 (t0) REVERT: C 868 ASP cc_start: 0.8421 (m-30) cc_final: 0.8070 (m-30) REVERT: C 941 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9139 (mp) REVERT: C 1146 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 1153 GLN cc_start: 0.9500 (pt0) cc_final: 0.9223 (pp30) REVERT: D 430 MET cc_start: 0.9088 (tpt) cc_final: 0.8786 (tpt) REVERT: D 431 ASP cc_start: 0.8855 (t0) cc_final: 0.8387 (t0) REVERT: D 868 ASP cc_start: 0.8430 (m-30) cc_final: 0.8081 (m-30) REVERT: D 941 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9113 (mp) REVERT: D 1146 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 89 outliers final: 66 residues processed: 423 average time/residue: 0.3759 time to fit residues: 263.1269 Evaluate side-chains 418 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 345 time to evaluate : 3.213 ------------------------------------------------------------------------------- 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 332 ARG Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 509 MET 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 789 SER 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 941 LEU Chi-restraints excluded: chain B residue 86 LYS 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 288 ILE 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 429 LEU 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 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 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 288 ILE 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 429 LEU 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 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 155 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 0.0670 chunk 122 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069488 restraints weight = 79166.168| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.26 r_work: 0.2804 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30752 Z= 0.232 Angle : 0.581 8.585 42320 Z= 0.288 Chirality : 0.038 0.134 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.565 22.204 4284 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 12.87 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.14), residues: 3832 helix: 2.48 (0.11), residues: 2444 sheet: -0.47 (0.35), residues: 236 loop : -0.75 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1058 HIS 0.007 0.001 HIS A1128 PHE 0.012 0.001 PHE C 931 TYR 0.011 0.001 TYR C 971 ARG 0.007 0.000 ARG C1136 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1892) hydrogen bonds : angle 4.21901 ( 5496) covalent geometry : bond 0.00531 (30752) covalent geometry : angle 0.58052 (42320) *********************** 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 434 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 336 time to evaluate : 3.164 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 86 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7660 (tppt) REVERT: A 430 MET cc_start: 0.9053 (tpt) cc_final: 0.8849 (tpt) REVERT: A 431 ASP cc_start: 0.8924 (t0) cc_final: 0.8483 (t0) REVERT: A 644 ARG cc_start: 0.6000 (tpt170) cc_final: 0.2808 (ttp80) REVERT: A 699 CYS cc_start: 0.8628 (m) cc_final: 0.7979 (t) REVERT: A 868 ASP cc_start: 0.8486 (m-30) cc_final: 0.7811 (m-30) REVERT: A 869 LEU cc_start: 0.9273 (mt) cc_final: 0.8879 (mt) REVERT: A 941 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9133 (mp) REVERT: A 1146 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 86 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7626 (tppt) REVERT: B 431 ASP cc_start: 0.8943 (t0) cc_final: 0.8515 (t0) REVERT: B 644 ARG cc_start: 0.5991 (tpt170) cc_final: 0.2793 (ttp80) REVERT: B 699 CYS cc_start: 0.8624 (m) cc_final: 0.7971 (t) REVERT: B 868 ASP cc_start: 0.8478 (m-30) cc_final: 0.7803 (m-30) REVERT: B 869 LEU cc_start: 0.9278 (mt) cc_final: 0.8881 (mt) REVERT: B 941 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 1146 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 431 ASP cc_start: 0.8944 (t0) cc_final: 0.8511 (t0) REVERT: C 644 ARG cc_start: 0.5965 (tpt170) cc_final: 0.2800 (ttp80) REVERT: C 699 CYS cc_start: 0.8627 (m) cc_final: 0.7980 (t) REVERT: C 868 ASP cc_start: 0.8487 (m-30) cc_final: 0.7813 (m-30) REVERT: C 869 LEU cc_start: 0.9281 (mt) cc_final: 0.8881 (mt) REVERT: C 941 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9144 (mp) REVERT: C 1146 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 1153 GLN cc_start: 0.9527 (pt0) cc_final: 0.9243 (pp30) REVERT: D 431 ASP cc_start: 0.8935 (t0) cc_final: 0.8508 (t0) REVERT: D 644 ARG cc_start: 0.5970 (tpt170) cc_final: 0.2803 (ttp80) REVERT: D 699 CYS cc_start: 0.8633 (m) cc_final: 0.7986 (t) REVERT: D 868 ASP cc_start: 0.8482 (m-30) cc_final: 0.7807 (m-30) REVERT: D 869 LEU cc_start: 0.9270 (mt) cc_final: 0.8881 (mt) REVERT: D 941 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9129 (mp) REVERT: D 1146 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8186 (tm-30) outliers start: 98 outliers final: 73 residues processed: 398 average time/residue: 0.3683 time to fit residues: 242.0976 Evaluate side-chains 396 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 3.150 ------------------------------------------------------------------------------- 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 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 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 86 LYS 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 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 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 934 LEU Chi-restraints excluded: chain B residue 941 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 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 781 THR Chi-restraints excluded: chain C residue 789 SER 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 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 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 107 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 308 optimal weight: 0.0270 chunk 118 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.071271 restraints weight = 78708.040| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.24 r_work: 0.2834 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30752 Z= 0.145 Angle : 0.537 8.860 42320 Z= 0.268 Chirality : 0.037 0.124 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.521 21.072 4284 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.26 % Allowed : 13.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2448 sheet: -0.42 (0.35), residues: 236 loop : -0.68 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.006 0.001 HIS A1128 PHE 0.010 0.001 PHE C 627 TYR 0.012 0.001 TYR A1063 ARG 0.007 0.000 ARG C1136 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 1892) hydrogen bonds : angle 4.10405 ( 5496) covalent geometry : bond 0.00330 (30752) covalent geometry : angle 0.53732 (42320) *********************** 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 445 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 349 time to evaluate : 3.574 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 86 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7633 (tppt) REVERT: A 431 ASP cc_start: 0.8905 (t0) cc_final: 0.8439 (t0) REVERT: A 644 ARG cc_start: 0.5976 (tpt170) cc_final: 0.2756 (ttp80) REVERT: A 699 CYS cc_start: 0.8549 (m) cc_final: 0.7854 (t) REVERT: A 868 ASP cc_start: 0.8472 (m-30) cc_final: 0.7765 (m-30) REVERT: A 941 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9114 (mp) REVERT: A 1146 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8171 (tm-30) REVERT: B 86 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7598 (tppt) REVERT: B 430 MET cc_start: 0.9047 (tpt) cc_final: 0.8794 (tpt) REVERT: B 431 ASP cc_start: 0.8810 (t0) cc_final: 0.8266 (t0) REVERT: B 644 ARG cc_start: 0.5971 (tpt170) cc_final: 0.2622 (tmm160) REVERT: B 699 CYS cc_start: 0.8543 (m) cc_final: 0.7842 (t) REVERT: B 868 ASP cc_start: 0.8462 (m-30) cc_final: 0.7753 (m-30) REVERT: B 941 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9116 (mp) REVERT: B 1146 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 86 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7630 (tppt) REVERT: C 430 MET cc_start: 0.9055 (tpt) cc_final: 0.8805 (tpt) REVERT: C 431 ASP cc_start: 0.8818 (t0) cc_final: 0.8274 (t0) REVERT: C 644 ARG cc_start: 0.5943 (tpt170) cc_final: 0.2619 (tmm160) REVERT: C 699 CYS cc_start: 0.8546 (m) cc_final: 0.7857 (t) REVERT: C 868 ASP cc_start: 0.8475 (m-30) cc_final: 0.7771 (m-30) REVERT: C 941 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9127 (mp) REVERT: C 1146 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 1153 GLN cc_start: 0.9515 (pt0) cc_final: 0.9244 (pp30) REVERT: D 86 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7650 (tppt) REVERT: D 430 MET cc_start: 0.9059 (tpt) cc_final: 0.8807 (tpt) REVERT: D 431 ASP cc_start: 0.8810 (t0) cc_final: 0.8263 (t0) REVERT: D 644 ARG cc_start: 0.5945 (tpt170) cc_final: 0.2634 (tmm160) REVERT: D 699 CYS cc_start: 0.8546 (m) cc_final: 0.7858 (t) REVERT: D 868 ASP cc_start: 0.8471 (m-30) cc_final: 0.7764 (m-30) REVERT: D 941 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9122 (mp) REVERT: D 1146 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8248 (tm-30) outliers start: 96 outliers final: 80 residues processed: 406 average time/residue: 0.3916 time to fit residues: 264.4812 Evaluate side-chains 422 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 334 time to evaluate : 3.217 ------------------------------------------------------------------------------- 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 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 440 PHE Chi-restraints excluded: chain A residue 509 MET 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 789 SER 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 A residue 981 GLU Chi-restraints excluded: chain B residue 86 LYS 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 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR 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 934 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 86 LYS 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 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 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 C residue 981 GLU Chi-restraints excluded: chain D residue 86 LYS 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 581 MET 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 Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 328 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 313 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS A1032 ASN B 350 GLN ** B1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 ASN ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 GLN D1032 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.069234 restraints weight = 79911.296| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.24 r_work: 0.2791 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 30752 Z= 0.260 Angle : 0.600 7.430 42320 Z= 0.301 Chirality : 0.039 0.237 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.604 22.543 4284 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.16 % Allowed : 13.62 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3832 helix: 2.44 (0.11), residues: 2432 sheet: -0.60 (0.35), residues: 236 loop : -0.68 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.007 0.001 HIS D1128 PHE 0.013 0.001 PHE A 627 TYR 0.013 0.001 TYR B 971 ARG 0.008 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 1892) hydrogen bonds : angle 4.26090 ( 5496) covalent geometry : bond 0.00594 (30752) covalent geometry : angle 0.59976 (42320) *********************** 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 424 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 331 time to evaluate : 3.453 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 86 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7661 (tppt) REVERT: A 430 MET cc_start: 0.9060 (tpt) cc_final: 0.8860 (tpp) REVERT: A 431 ASP cc_start: 0.8850 (t0) cc_final: 0.8319 (t0) REVERT: A 644 ARG cc_start: 0.5846 (tpt170) cc_final: 0.2703 (ttp80) REVERT: A 699 CYS cc_start: 0.8628 (m) cc_final: 0.8004 (t) REVERT: A 868 ASP cc_start: 0.8495 (m-30) cc_final: 0.7781 (m-30) REVERT: A 941 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9123 (mp) REVERT: A 1146 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 86 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7652 (tppt) REVERT: B 430 MET cc_start: 0.9053 (tpt) cc_final: 0.8839 (tpp) REVERT: B 431 ASP cc_start: 0.8888 (t0) cc_final: 0.8397 (t0) REVERT: B 644 ARG cc_start: 0.5842 (tpt170) cc_final: 0.2662 (ttp80) REVERT: B 699 CYS cc_start: 0.8646 (m) cc_final: 0.7999 (t) REVERT: B 868 ASP cc_start: 0.8483 (m-30) cc_final: 0.7764 (m-30) REVERT: B 941 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9122 (mp) REVERT: B 1146 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 86 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7658 (tppt) REVERT: C 430 MET cc_start: 0.9058 (tpt) cc_final: 0.8835 (tpp) REVERT: C 431 ASP cc_start: 0.8898 (t0) cc_final: 0.8403 (t0) REVERT: C 644 ARG cc_start: 0.5809 (tpt170) cc_final: 0.2655 (ttp80) REVERT: C 699 CYS cc_start: 0.8642 (m) cc_final: 0.8005 (t) REVERT: C 868 ASP cc_start: 0.8494 (m-30) cc_final: 0.7777 (m-30) REVERT: C 941 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9133 (mp) REVERT: C 1146 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 1153 GLN cc_start: 0.9511 (pt0) cc_final: 0.9255 (pp30) REVERT: D 86 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7661 (tppt) REVERT: D 430 MET cc_start: 0.9058 (tpt) cc_final: 0.8844 (tpp) REVERT: D 431 ASP cc_start: 0.8893 (t0) cc_final: 0.8401 (t0) REVERT: D 644 ARG cc_start: 0.5815 (tpt170) cc_final: 0.2672 (ttp80) REVERT: D 699 CYS cc_start: 0.8657 (m) cc_final: 0.8022 (t) REVERT: D 868 ASP cc_start: 0.8499 (m-30) cc_final: 0.7783 (m-30) REVERT: D 941 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9129 (mp) REVERT: D 1146 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8188 (tm-30) outliers start: 93 outliers final: 73 residues processed: 390 average time/residue: 0.3826 time to fit residues: 247.8305 Evaluate side-chains 405 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 324 time to evaluate : 3.210 ------------------------------------------------------------------------------- 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 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 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 86 LYS 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 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR 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 934 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 86 LYS 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 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 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 86 LYS 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 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 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 163 optimal weight: 0.9980 chunk 376 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 312 optimal weight: 30.0000 chunk 304 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071506 restraints weight = 78853.238| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.25 r_work: 0.2835 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30752 Z= 0.125 Angle : 0.538 8.220 42320 Z= 0.268 Chirality : 0.037 0.215 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.525 20.498 4284 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.79 % Allowed : 14.30 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3832 helix: 2.52 (0.11), residues: 2452 sheet: -0.49 (0.34), residues: 236 loop : -0.65 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1058 HIS 0.006 0.001 HIS A1128 PHE 0.013 0.001 PHE A 627 TYR 0.013 0.001 TYR D1063 ARG 0.013 0.000 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 1892) hydrogen bonds : angle 4.07294 ( 5496) covalent geometry : bond 0.00282 (30752) covalent geometry : angle 0.53786 (42320) *********************** 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 436 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 3.195 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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: 0.8147 (OUTLIER) cc_final: 0.7631 (tppt) REVERT: A 430 MET cc_start: 0.9072 (tpt) cc_final: 0.8851 (tpp) REVERT: A 431 ASP cc_start: 0.8806 (t0) cc_final: 0.8250 (t0) REVERT: A 644 ARG cc_start: 0.5844 (tpt170) cc_final: 0.2681 (ttp80) REVERT: A 699 CYS cc_start: 0.8513 (m) cc_final: 0.7827 (t) REVERT: A 868 ASP cc_start: 0.8459 (m-30) cc_final: 0.7758 (m-30) REVERT: A 941 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 1146 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 86 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7614 (tppt) REVERT: B 431 ASP cc_start: 0.8818 (t0) cc_final: 0.8267 (t0) REVERT: B 644 ARG cc_start: 0.5908 (tpt170) cc_final: 0.2732 (ttp80) REVERT: B 699 CYS cc_start: 0.8488 (m) cc_final: 0.7798 (t) REVERT: B 868 ASP cc_start: 0.8448 (m-30) cc_final: 0.7745 (m-30) REVERT: B 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 1146 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 86 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7615 (tppt) REVERT: C 430 MET cc_start: 0.9101 (tpt) cc_final: 0.8889 (tpp) REVERT: C 431 ASP cc_start: 0.8828 (t0) cc_final: 0.8282 (t0) REVERT: C 644 ARG cc_start: 0.5892 (tpt170) cc_final: 0.2733 (ttp80) REVERT: C 868 ASP cc_start: 0.8458 (m-30) cc_final: 0.7759 (m-30) REVERT: C 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9096 (mp) REVERT: C 1146 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 1153 GLN cc_start: 0.9489 (pt0) cc_final: 0.9236 (pp30) REVERT: D 86 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7615 (tppt) REVERT: D 431 ASP cc_start: 0.8820 (t0) cc_final: 0.8269 (t0) REVERT: D 644 ARG cc_start: 0.5885 (tpt170) cc_final: 0.2745 (ttp80) REVERT: D 699 CYS cc_start: 0.8481 (m) cc_final: 0.7805 (t) REVERT: D 868 ASP cc_start: 0.8468 (m-30) cc_final: 0.7773 (m-30) REVERT: D 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9100 (mp) REVERT: D 1146 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8192 (tm-30) outliers start: 82 outliers final: 73 residues processed: 406 average time/residue: 0.3827 time to fit residues: 258.2288 Evaluate side-chains 430 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 3.175 ------------------------------------------------------------------------------- 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 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 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 86 LYS 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 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 86 LYS 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 622 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 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 86 LYS 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 581 MET Chi-restraints excluded: chain D residue 622 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 100 optimal weight: 50.0000 chunk 199 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 299 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070985 restraints weight = 78877.193| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.30 r_work: 0.2832 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30752 Z= 0.142 Angle : 0.547 8.487 42320 Z= 0.272 Chirality : 0.037 0.209 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.502 20.780 4284 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.96 % Allowed : 14.81 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.14), residues: 3832 helix: 2.49 (0.11), residues: 2452 sheet: -0.48 (0.35), residues: 236 loop : -0.62 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.005 0.001 HIS C1128 PHE 0.012 0.001 PHE A 627 TYR 0.012 0.001 TYR D1063 ARG 0.011 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 1892) hydrogen bonds : angle 4.05971 ( 5496) covalent geometry : bond 0.00324 (30752) covalent geometry : angle 0.54694 (42320) ********************** 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 443 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 356 time to evaluate : 3.234 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. 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 86 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7661 (tppt) REVERT: A 430 MET cc_start: 0.9099 (tpt) cc_final: 0.8874 (tpp) REVERT: A 431 ASP cc_start: 0.8812 (t0) cc_final: 0.8274 (t0) REVERT: A 644 ARG cc_start: 0.5782 (tpt170) cc_final: 0.2641 (ttp80) REVERT: A 868 ASP cc_start: 0.8471 (m-30) cc_final: 0.7773 (m-30) REVERT: A 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 1146 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8241 (tm-30) REVERT: B 86 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7633 (tppt) REVERT: B 431 ASP cc_start: 0.8742 (t0) cc_final: 0.8214 (t0) REVERT: B 644 ARG cc_start: 0.5801 (tpt170) cc_final: 0.2654 (ttp80) REVERT: B 868 ASP cc_start: 0.8452 (m-30) cc_final: 0.7751 (m-30) REVERT: B 941 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9107 (mp) REVERT: B 1146 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 86 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7629 (tppt) REVERT: C 431 ASP cc_start: 0.8835 (t0) cc_final: 0.8297 (t0) REVERT: C 644 ARG cc_start: 0.5787 (tpt170) cc_final: 0.2658 (ttp80) REVERT: C 868 ASP cc_start: 0.8467 (m-30) cc_final: 0.7769 (m-30) REVERT: C 941 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9115 (mp) REVERT: C 1146 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 1153 GLN cc_start: 0.9480 (pt0) cc_final: 0.9240 (pp30) REVERT: D 86 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7629 (tppt) REVERT: D 431 ASP cc_start: 0.8742 (t0) cc_final: 0.8218 (t0) REVERT: D 644 ARG cc_start: 0.5749 (tpt170) cc_final: 0.2618 (ttp80) REVERT: D 868 ASP cc_start: 0.8489 (m-30) cc_final: 0.7794 (m-30) REVERT: D 941 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9117 (mp) REVERT: D 1146 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8195 (tm-30) outliers start: 87 outliers final: 76 residues processed: 408 average time/residue: 0.3824 time to fit residues: 258.3594 Evaluate side-chains 428 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 344 time to evaluate : 3.485 ------------------------------------------------------------------------------- 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 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 789 SER 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 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 86 LYS 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 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 86 LYS 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 622 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 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 86 LYS 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 581 MET Chi-restraints excluded: chain D residue 622 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 164 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 215 optimal weight: 0.0980 chunk 209 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 375 optimal weight: 0.9990 chunk 386 optimal weight: 0.9990 chunk 335 optimal weight: 10.0000 chunk 267 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073145 restraints weight = 78779.564| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.28 r_work: 0.2869 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 30752 Z= 0.111 Angle : 0.536 8.683 42320 Z= 0.266 Chirality : 0.036 0.225 4768 Planarity : 0.004 0.050 5232 Dihedral : 3.471 19.665 4284 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.55 % Allowed : 15.22 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2448 sheet: -0.39 (0.35), residues: 236 loop : -0.62 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1058 HIS 0.005 0.001 HIS A1128 PHE 0.012 0.001 PHE A 627 TYR 0.012 0.001 TYR A1063 ARG 0.004 0.000 ARG D 336 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 1892) hydrogen bonds : angle 3.98565 ( 5496) covalent geometry : bond 0.00246 (30752) covalent geometry : angle 0.53635 (42320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14030.22 seconds wall clock time: 243 minutes 34.12 seconds (14614.12 seconds total)