Starting phenix.real_space_refine on Mon Aug 25 18:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8y_44362/08_2025/9b8y_44362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8y_44362/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b8y_44362/08_2025/9b8y_44362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8y_44362/08_2025/9b8y_44362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b8y_44362/08_2025/9b8y_44362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8y_44362/08_2025/9b8y_44362.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 V 40 8.30 5 S 152 5.16 5 C 19340 2.51 5 N 5232 2.21 5 O 5208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 4, 'ARG:plan': 14, 'ASP:plan': 16, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 228 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 9.31, per 1000 atoms: 0.31 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: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 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: 6.12 Time building geometry restraints manager: 4.15 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.580 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.610 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.15), residues: 3832 helix: 2.80 (0.11), residues: 2432 sheet: -0.17 (0.39), residues: 200 loop : -0.63 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 442 TYR 0.007 0.001 TYR A1063 PHE 0.013 0.001 PHE B 931 TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00442 (30752) covalent geometry : angle 0.47491 (42320) hydrogen bonds : bond 0.12248 ( 1892) hydrogen bonds : angle 5.01710 ( 5496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 490 time to evaluate : 1.188 Fit side-chains TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 254 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 332 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8692 (ttm170) REVERT: A 431 ASP cc_start: 0.8518 (t0) cc_final: 0.8207 (t0) REVERT: A 622 MET cc_start: 0.8020 (mtp) cc_final: 0.7782 (mtp) REVERT: B 254 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 332 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8613 (ttm170) REVERT: B 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8227 (t0) REVERT: C 254 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 332 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8592 (ttm170) REVERT: C 431 ASP cc_start: 0.8526 (t0) cc_final: 0.8211 (t0) REVERT: C 1153 GLN cc_start: 0.9281 (pt0) cc_final: 0.9078 (pp30) REVERT: D 254 GLU cc_start: 0.8070 (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: 0.2017 time to fit residues: 158.9350 Evaluate side-chains 329 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 D1017 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073555 restraints weight = 78533.563| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.23 r_work: 0.2875 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30752 Z= 0.132 Angle : 0.547 7.908 42320 Z= 0.277 Chirality : 0.038 0.224 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.466 15.705 4284 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.94 % Allowed : 8.93 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.14), residues: 3832 helix: 2.72 (0.11), residues: 2424 sheet: 0.11 (0.37), residues: 236 loop : -0.64 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 857 TYR 0.017 0.001 TYR A 103 PHE 0.015 0.001 PHE A 902 TRP 0.010 0.001 TRP A1058 HIS 0.008 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00293 (30752) covalent geometry : angle 0.54710 (42320) hydrogen bonds : bond 0.04370 ( 1892) hydrogen bonds : angle 4.20910 ( 5496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 426 time to evaluate : 1.029 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 254 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 430 MET cc_start: 0.9015 (tpt) cc_final: 0.8760 (tpp) REVERT: A 431 ASP cc_start: 0.8775 (t0) cc_final: 0.8273 (t0) REVERT: A 868 ASP cc_start: 0.8300 (m-30) cc_final: 0.7805 (m-30) REVERT: A 1146 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8149 (tm-30) REVERT: B 254 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 430 MET cc_start: 0.9041 (tpt) cc_final: 0.8781 (tpp) REVERT: B 431 ASP cc_start: 0.8794 (t0) cc_final: 0.8316 (t0) REVERT: B 670 ASP cc_start: 0.8972 (m-30) cc_final: 0.8294 (m-30) REVERT: B 868 ASP cc_start: 0.8304 (m-30) cc_final: 0.7810 (m-30) REVERT: B 1146 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7990 (tm-30) REVERT: C 254 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 430 MET cc_start: 0.9046 (tpt) cc_final: 0.8789 (tpp) REVERT: C 431 ASP cc_start: 0.8797 (t0) cc_final: 0.8322 (t0) REVERT: C 868 ASP cc_start: 0.8302 (m-30) cc_final: 0.7808 (m-30) REVERT: C 1146 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 1153 GLN cc_start: 0.9507 (pt0) cc_final: 0.9215 (pp30) REVERT: D 254 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7723 (mt-10) REVERT: D 430 MET cc_start: 0.9052 (tpt) cc_final: 0.8793 (tpp) REVERT: D 431 ASP cc_start: 0.8784 (t0) cc_final: 0.8311 (t0) REVERT: D 868 ASP cc_start: 0.8310 (m-30) cc_final: 0.8062 (m-30) REVERT: D 1146 GLU cc_start: 0.8629 (tm-30) cc_final: 0.7981 (tm-30) outliers start: 57 outliers final: 39 residues processed: 457 average time/residue: 0.1642 time to fit residues: 122.7913 Evaluate side-chains 385 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 930 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 301 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 chunk 267 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 0.2980 chunk 371 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073720 restraints weight = 78159.688| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.24 r_work: 0.2888 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30752 Z= 0.112 Angle : 0.525 9.220 42320 Z= 0.260 Chirality : 0.036 0.141 4768 Planarity : 0.004 0.059 5232 Dihedral : 3.433 15.542 4284 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 11.11 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.14), residues: 3832 helix: 2.64 (0.11), residues: 2420 sheet: -0.04 (0.35), residues: 260 loop : -0.64 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1147 TYR 0.018 0.001 TYR B 103 PHE 0.010 0.001 PHE C 902 TRP 0.009 0.001 TRP A1058 HIS 0.007 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00248 (30752) covalent geometry : angle 0.52519 (42320) hydrogen bonds : bond 0.03880 ( 1892) hydrogen bonds : angle 4.02964 ( 5496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 425 time to evaluate : 1.261 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 254 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7848 (mt-10) REVERT: A 431 ASP cc_start: 0.8789 (t0) cc_final: 0.8330 (t0) REVERT: A 868 ASP cc_start: 0.8359 (m-30) cc_final: 0.7799 (m-30) REVERT: A 941 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9122 (mp) REVERT: A 1146 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 254 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7770 (mt-10) REVERT: B 431 ASP cc_start: 0.8798 (t0) cc_final: 0.8350 (t0) REVERT: B 868 ASP cc_start: 0.8358 (m-30) cc_final: 0.7795 (m-30) REVERT: B 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9123 (mp) REVERT: B 1146 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8016 (tm-30) REVERT: C 254 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 431 ASP cc_start: 0.8804 (t0) cc_final: 0.8352 (t0) REVERT: C 868 ASP cc_start: 0.8360 (m-30) cc_final: 0.7801 (m-30) REVERT: C 941 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9120 (mp) REVERT: C 1146 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7991 (tm-30) REVERT: C 1149 LYS cc_start: 0.9034 (tppt) cc_final: 0.8341 (tppt) REVERT: C 1153 GLN cc_start: 0.9524 (pt0) cc_final: 0.9230 (pp30) REVERT: D 254 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 431 ASP cc_start: 0.8787 (t0) cc_final: 0.8338 (t0) REVERT: D 868 ASP cc_start: 0.8357 (m-30) cc_final: 0.7797 (m-30) REVERT: D 941 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9120 (mp) REVERT: D 1146 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8001 (tm-30) outliers start: 88 outliers final: 62 residues processed: 475 average time/residue: 0.1801 time to fit residues: 140.8766 Evaluate side-chains 432 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 804 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 804 ASP Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 407 ASP 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 789 SER Chi-restraints excluded: chain C residue 804 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 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 509 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 804 ASP Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 384 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 149 optimal weight: 4.9990 chunk 245 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.101225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070493 restraints weight = 78915.584| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.18 r_work: 0.2813 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30752 Z= 0.248 Angle : 0.593 8.152 42320 Z= 0.296 Chirality : 0.039 0.139 4768 Planarity : 0.005 0.050 5232 Dihedral : 3.565 21.148 4284 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.02 % Allowed : 11.89 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.14), residues: 3832 helix: 2.52 (0.11), residues: 2424 sheet: -0.33 (0.35), residues: 236 loop : -0.71 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1136 TYR 0.011 0.001 TYR A 577 PHE 0.014 0.001 PHE A 931 TRP 0.011 0.001 TRP C1124 HIS 0.008 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00572 (30752) covalent geometry : angle 0.59318 (42320) hydrogen bonds : bond 0.04475 ( 1892) hydrogen bonds : angle 4.25330 ( 5496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 336 time to evaluate : 1.140 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7700 (tppt) REVERT: A 430 MET cc_start: 0.9076 (tpt) cc_final: 0.8780 (tpt) REVERT: A 431 ASP cc_start: 0.8887 (t0) cc_final: 0.8429 (t0) REVERT: A 868 ASP cc_start: 0.8386 (m-30) cc_final: 0.8092 (m-30) REVERT: A 869 LEU cc_start: 0.9257 (mt) cc_final: 0.8872 (mt) REVERT: A 941 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 1146 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 430 MET cc_start: 0.9067 (tpt) cc_final: 0.8764 (tpt) REVERT: B 431 ASP cc_start: 0.8904 (t0) cc_final: 0.8452 (t0) REVERT: B 868 ASP cc_start: 0.8386 (m-30) cc_final: 0.8087 (m-30) REVERT: B 869 LEU cc_start: 0.9263 (mt) cc_final: 0.8895 (mt) REVERT: B 941 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9116 (mp) REVERT: B 1140 LYS cc_start: 0.9377 (tppp) cc_final: 0.9171 (tppp) REVERT: B 1146 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7973 (tm-30) REVERT: C 430 MET cc_start: 0.9074 (tpt) cc_final: 0.8775 (tpt) REVERT: C 431 ASP cc_start: 0.8904 (t0) cc_final: 0.8468 (t0) REVERT: C 699 CYS cc_start: 0.8607 (m) cc_final: 0.7932 (t) REVERT: C 868 ASP cc_start: 0.8393 (m-30) cc_final: 0.8099 (m-30) REVERT: C 869 LEU cc_start: 0.9262 (mt) cc_final: 0.8877 (mt) REVERT: C 941 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9118 (mp) REVERT: C 1140 LYS cc_start: 0.9374 (tppp) cc_final: 0.9169 (tppp) REVERT: C 1146 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 1153 GLN cc_start: 0.9529 (pt0) cc_final: 0.9229 (pp30) REVERT: D 430 MET cc_start: 0.9077 (tpt) cc_final: 0.8774 (tpt) REVERT: D 431 ASP cc_start: 0.8894 (t0) cc_final: 0.8445 (t0) REVERT: D 868 ASP cc_start: 0.8396 (m-30) cc_final: 0.8098 (m-30) REVERT: D 869 LEU cc_start: 0.9263 (mt) cc_final: 0.8892 (mt) REVERT: D 941 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9117 (mp) REVERT: D 1140 LYS cc_start: 0.9391 (tppp) cc_final: 0.9186 (tppp) REVERT: D 1146 GLU cc_start: 0.8602 (tm-30) cc_final: 0.7975 (tm-30) outliers start: 89 outliers final: 61 residues processed: 390 average time/residue: 0.1682 time to fit residues: 108.3888 Evaluate side-chains 387 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 321 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 934 LEU 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 309 ASP Chi-restraints excluded: chain C residue 407 ASP 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 792 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 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 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 325 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 352 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 chunk 308 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3674 r_free = 0.3674 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.073119 restraints weight = 78374.957| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.22 r_work: 0.2868 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30752 Z= 0.113 Angle : 0.522 9.578 42320 Z= 0.259 Chirality : 0.036 0.127 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.510 21.018 4284 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.55 % Allowed : 13.18 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.14), residues: 3832 helix: 2.57 (0.11), residues: 2440 sheet: -0.27 (0.35), residues: 236 loop : -0.74 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1136 TYR 0.012 0.001 TYR B1063 PHE 0.014 0.001 PHE A 627 TRP 0.010 0.001 TRP A1058 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00248 (30752) covalent geometry : angle 0.52248 (42320) hydrogen bonds : bond 0.03883 ( 1892) hydrogen bonds : angle 4.02773 ( 5496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 372 time to evaluate : 1.148 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: 0.8147 (OUTLIER) cc_final: 0.7654 (tppt) REVERT: A 332 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8612 (ttp80) REVERT: A 430 MET cc_start: 0.9079 (tpt) cc_final: 0.8844 (tpt) REVERT: A 431 ASP cc_start: 0.8854 (t0) cc_final: 0.8371 (t0) REVERT: A 868 ASP cc_start: 0.8380 (m-30) cc_final: 0.8007 (m-30) REVERT: A 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9104 (mp) REVERT: A 1146 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 254 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 430 MET cc_start: 0.9058 (tpt) cc_final: 0.8824 (tpt) REVERT: B 431 ASP cc_start: 0.8872 (t0) cc_final: 0.8406 (t0) REVERT: B 868 ASP cc_start: 0.8385 (m-30) cc_final: 0.8015 (m-30) REVERT: B 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9089 (mp) REVERT: B 1140 LYS cc_start: 0.9387 (tppp) cc_final: 0.9166 (tmtt) REVERT: B 1146 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 254 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7802 (mt-10) REVERT: C 430 MET cc_start: 0.9068 (tpt) cc_final: 0.8828 (tpt) REVERT: C 431 ASP cc_start: 0.8883 (t0) cc_final: 0.8418 (t0) REVERT: C 868 ASP cc_start: 0.8390 (m-30) cc_final: 0.8021 (m-30) REVERT: C 941 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9105 (mp) REVERT: C 1140 LYS cc_start: 0.9388 (tppp) cc_final: 0.9145 (tppp) REVERT: C 1146 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 1153 GLN cc_start: 0.9504 (pt0) cc_final: 0.9218 (pp30) REVERT: D 254 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7804 (mt-10) REVERT: D 430 MET cc_start: 0.9073 (tpt) cc_final: 0.8838 (tpt) REVERT: D 431 ASP cc_start: 0.8867 (t0) cc_final: 0.8408 (t0) REVERT: D 868 ASP cc_start: 0.8411 (m-30) cc_final: 0.8044 (m-30) REVERT: D 941 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9103 (mp) REVERT: D 1140 LYS cc_start: 0.9409 (tppp) cc_final: 0.9168 (tppp) REVERT: D 1146 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8140 (tm-30) outliers start: 75 outliers final: 58 residues processed: 417 average time/residue: 0.1867 time to fit residues: 129.1483 Evaluate side-chains 418 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 354 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 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 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 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 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 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 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 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 306 optimal weight: 9.9990 chunk 256 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 325 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS A 669 GLN B 350 GLN C 350 GLN C 669 GLN D 350 GLN D 669 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.068662 restraints weight = 79563.083| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.22 r_work: 0.2786 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 30752 Z= 0.285 Angle : 0.619 8.625 42320 Z= 0.309 Chirality : 0.040 0.143 4768 Planarity : 0.005 0.048 5232 Dihedral : 3.611 22.952 4284 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.33 % Allowed : 12.67 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.14), residues: 3832 helix: 2.46 (0.11), residues: 2428 sheet: -0.39 (0.35), residues: 236 loop : -0.74 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1136 TYR 0.011 0.001 TYR A 464 PHE 0.015 0.001 PHE A 931 TRP 0.011 0.001 TRP A 649 HIS 0.007 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00657 (30752) covalent geometry : angle 0.61929 (42320) hydrogen bonds : bond 0.04656 ( 1892) hydrogen bonds : angle 4.27906 ( 5496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 337 time to evaluate : 1.189 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: 0.8194 (OUTLIER) cc_final: 0.7694 (tppt) REVERT: A 431 ASP cc_start: 0.8968 (t0) cc_final: 0.8537 (t0) REVERT: A 644 ARG cc_start: 0.5873 (tpt170) cc_final: 0.2786 (ttp80) REVERT: A 699 CYS cc_start: 0.8662 (m) cc_final: 0.8024 (t) REVERT: A 868 ASP cc_start: 0.8459 (m-30) cc_final: 0.7774 (m-30) REVERT: A 941 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9143 (mp) REVERT: A 1146 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8558 (tm-30) REVERT: B 254 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 431 ASP cc_start: 0.8974 (t0) cc_final: 0.8531 (t0) REVERT: B 644 ARG cc_start: 0.5923 (tpt170) cc_final: 0.2816 (ttp80) REVERT: B 699 CYS cc_start: 0.8656 (m) cc_final: 0.8016 (t) REVERT: B 868 ASP cc_start: 0.8457 (m-30) cc_final: 0.7770 (m-30) REVERT: B 941 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 1140 LYS cc_start: 0.9412 (tppp) cc_final: 0.9157 (tppp) REVERT: B 1146 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8157 (tm-30) REVERT: C 431 ASP cc_start: 0.8975 (t0) cc_final: 0.8534 (t0) REVERT: C 644 ARG cc_start: 0.5869 (tpt170) cc_final: 0.2772 (ttp80) REVERT: C 699 CYS cc_start: 0.8645 (m) cc_final: 0.8000 (t) REVERT: C 868 ASP cc_start: 0.8465 (m-30) cc_final: 0.7780 (m-30) REVERT: C 941 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9147 (mp) REVERT: C 1140 LYS cc_start: 0.9417 (tppp) cc_final: 0.9163 (tppp) REVERT: C 1146 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8160 (tm-30) REVERT: C 1153 GLN cc_start: 0.9523 (pt0) cc_final: 0.9257 (pp30) REVERT: D 254 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 431 ASP cc_start: 0.8975 (t0) cc_final: 0.8538 (t0) REVERT: D 644 ARG cc_start: 0.5878 (tpt170) cc_final: 0.2768 (ttp80) REVERT: D 699 CYS cc_start: 0.8668 (m) cc_final: 0.8025 (t) REVERT: D 868 ASP cc_start: 0.8465 (m-30) cc_final: 0.7782 (m-30) REVERT: D 941 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9149 (mp) REVERT: D 1146 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8010 (tm-30) outliers start: 98 outliers final: 66 residues processed: 393 average time/residue: 0.1805 time to fit residues: 118.1620 Evaluate side-chains 393 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 322 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 125 SER 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 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 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 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 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 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 934 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 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 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 934 LEU Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 78 optimal weight: 0.9990 chunk 369 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 288 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.103283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.072552 restraints weight = 78175.361| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.20 r_work: 0.2857 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30752 Z= 0.113 Angle : 0.542 8.943 42320 Z= 0.270 Chirality : 0.037 0.239 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.536 20.757 4284 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.99 % Allowed : 14.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.14), residues: 3832 helix: 2.46 (0.11), residues: 2452 sheet: -0.26 (0.35), residues: 236 loop : -0.67 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1136 TYR 0.013 0.001 TYR B1063 PHE 0.015 0.001 PHE A 627 TRP 0.011 0.001 TRP C1058 HIS 0.006 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00244 (30752) covalent geometry : angle 0.54221 (42320) hydrogen bonds : bond 0.03968 ( 1892) hydrogen bonds : angle 4.05437 ( 5496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 360 time to evaluate : 1.210 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: 0.8131 (OUTLIER) cc_final: 0.7632 (tppt) REVERT: A 430 MET cc_start: 0.9030 (tpt) cc_final: 0.8816 (tpp) REVERT: A 431 ASP cc_start: 0.8803 (t0) cc_final: 0.8247 (t0) REVERT: A 644 ARG cc_start: 0.5953 (tpt170) cc_final: 0.2629 (tmm160) REVERT: A 699 CYS cc_start: 0.8510 (m) cc_final: 0.7827 (t) REVERT: A 868 ASP cc_start: 0.8442 (m-30) cc_final: 0.7734 (m-30) REVERT: A 941 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9107 (mp) REVERT: A 1140 LYS cc_start: 0.9261 (tmtt) cc_final: 0.9024 (tmtt) REVERT: A 1146 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 430 MET cc_start: 0.9020 (tpt) cc_final: 0.8801 (tpp) REVERT: B 431 ASP cc_start: 0.8812 (t0) cc_final: 0.8268 (t0) REVERT: B 644 ARG cc_start: 0.5940 (tpt170) cc_final: 0.2595 (tmm160) REVERT: B 699 CYS cc_start: 0.8512 (m) cc_final: 0.7808 (t) REVERT: B 868 ASP cc_start: 0.8444 (m-30) cc_final: 0.7740 (m-30) REVERT: B 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9094 (mp) REVERT: B 1140 LYS cc_start: 0.9386 (tppp) cc_final: 0.9144 (tmtt) REVERT: B 1146 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8125 (tm-30) REVERT: C 332 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8575 (ttm170) REVERT: C 430 MET cc_start: 0.9026 (tpt) cc_final: 0.8802 (tpp) REVERT: C 431 ASP cc_start: 0.8833 (t0) cc_final: 0.8286 (t0) REVERT: C 644 ARG cc_start: 0.5914 (tpt170) cc_final: 0.2561 (tmm160) REVERT: C 699 CYS cc_start: 0.8490 (m) cc_final: 0.7825 (t) REVERT: C 868 ASP cc_start: 0.8444 (m-30) cc_final: 0.7738 (m-30) REVERT: C 941 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9105 (mp) REVERT: C 1146 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 1153 GLN cc_start: 0.9499 (pt0) cc_final: 0.9243 (pp30) REVERT: D 430 MET cc_start: 0.9025 (tpt) cc_final: 0.8771 (tpp) REVERT: D 431 ASP cc_start: 0.8805 (t0) cc_final: 0.8260 (t0) REVERT: D 644 ARG cc_start: 0.5938 (tpt170) cc_final: 0.2583 (tmm160) REVERT: D 699 CYS cc_start: 0.8519 (m) cc_final: 0.7819 (t) REVERT: D 868 ASP cc_start: 0.8454 (m-30) cc_final: 0.7747 (m-30) REVERT: D 941 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9115 (mp) REVERT: D 1140 LYS cc_start: 0.9403 (tppp) cc_final: 0.9170 (tmtt) REVERT: D 1146 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8206 (tm-30) outliers start: 88 outliers final: 72 residues processed: 419 average time/residue: 0.1793 time to fit residues: 125.2669 Evaluate side-chains 423 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 345 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 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 A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 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 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 B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 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 105 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 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 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 269 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 308 optimal weight: 0.4980 chunk 78 optimal weight: 0.0970 chunk 372 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.102259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.070858 restraints weight = 78763.687| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.25 r_work: 0.2835 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30752 Z= 0.163 Angle : 0.539 7.694 42320 Z= 0.270 Chirality : 0.037 0.196 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.497 21.178 4284 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.92 % Allowed : 13.82 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.14), residues: 3832 helix: 2.47 (0.11), residues: 2456 sheet: -0.31 (0.35), residues: 236 loop : -0.64 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1136 TYR 0.010 0.001 TYR B1063 PHE 0.012 0.001 PHE A 627 TRP 0.010 0.001 TRP C1058 HIS 0.006 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00375 (30752) covalent geometry : angle 0.53936 (42320) hydrogen bonds : bond 0.04046 ( 1892) hydrogen bonds : angle 4.05915 ( 5496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 1.300 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: 0.8135 (OUTLIER) cc_final: 0.7650 (tppt) REVERT: A 430 MET cc_start: 0.9053 (tpt) cc_final: 0.8846 (tpp) REVERT: A 431 ASP cc_start: 0.8861 (t0) cc_final: 0.8314 (t0) REVERT: A 644 ARG cc_start: 0.5967 (tpt170) cc_final: 0.2609 (tmm160) REVERT: A 868 ASP cc_start: 0.8466 (m-30) cc_final: 0.7776 (m-30) REVERT: A 941 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9129 (mp) REVERT: A 1146 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 430 MET cc_start: 0.9053 (tpt) cc_final: 0.8840 (tpp) REVERT: B 431 ASP cc_start: 0.8872 (t0) cc_final: 0.8323 (t0) REVERT: B 644 ARG cc_start: 0.6041 (tpt170) cc_final: 0.2674 (tmm160) REVERT: B 868 ASP cc_start: 0.8462 (m-30) cc_final: 0.7772 (m-30) REVERT: B 941 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9138 (mp) REVERT: B 1140 LYS cc_start: 0.9412 (tppp) cc_final: 0.9138 (tppp) REVERT: B 1146 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 430 MET cc_start: 0.9047 (tpt) cc_final: 0.8828 (tpp) REVERT: C 431 ASP cc_start: 0.8888 (t0) cc_final: 0.8340 (t0) REVERT: C 644 ARG cc_start: 0.5966 (tpt170) cc_final: 0.2587 (tmm160) REVERT: C 699 CYS cc_start: 0.8557 (m) cc_final: 0.7857 (t) REVERT: C 868 ASP cc_start: 0.8464 (m-30) cc_final: 0.7775 (m-30) REVERT: C 941 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9145 (mp) REVERT: C 1140 LYS cc_start: 0.9419 (tppp) cc_final: 0.9146 (tppp) REVERT: C 1146 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 1153 GLN cc_start: 0.9504 (pt0) cc_final: 0.9246 (pp30) REVERT: D 430 MET cc_start: 0.9046 (tpt) cc_final: 0.8830 (tpp) REVERT: D 431 ASP cc_start: 0.8871 (t0) cc_final: 0.8323 (t0) REVERT: D 644 ARG cc_start: 0.5985 (tpt170) cc_final: 0.2615 (tmm160) REVERT: D 868 ASP cc_start: 0.8469 (m-30) cc_final: 0.7779 (m-30) REVERT: D 941 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9131 (mp) REVERT: D 1146 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8085 (tm-30) outliers start: 86 outliers final: 76 residues processed: 399 average time/residue: 0.1797 time to fit residues: 120.1219 Evaluate side-chains 412 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 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 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 75 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 321 optimal weight: 0.0470 chunk 326 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 234 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 363 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.104241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073506 restraints weight = 78261.658| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.25 r_work: 0.2880 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30752 Z= 0.108 Angle : 0.529 7.920 42320 Z= 0.264 Chirality : 0.037 0.231 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.448 19.195 4284 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.51 % Allowed : 14.88 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.14), residues: 3832 helix: 2.50 (0.11), residues: 2452 sheet: -0.26 (0.35), residues: 236 loop : -0.59 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 108 TYR 0.012 0.001 TYR B1063 PHE 0.011 0.001 PHE A 627 TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00230 (30752) covalent geometry : angle 0.52872 (42320) hydrogen bonds : bond 0.03671 ( 1892) hydrogen bonds : angle 3.96323 ( 5496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 391 time to evaluate : 1.387 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.8120 (OUTLIER) cc_final: 0.7626 (tppt) REVERT: A 430 MET cc_start: 0.9090 (tpt) cc_final: 0.8877 (tpp) REVERT: A 431 ASP cc_start: 0.8834 (t0) cc_final: 0.8261 (t0) REVERT: A 868 ASP cc_start: 0.8415 (m-30) cc_final: 0.7691 (m-30) REVERT: A 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9092 (mp) REVERT: A 1146 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 430 MET cc_start: 0.9093 (tpt) cc_final: 0.8880 (tpp) REVERT: B 431 ASP cc_start: 0.8828 (t0) cc_final: 0.8252 (t0) REVERT: B 868 ASP cc_start: 0.8418 (m-30) cc_final: 0.7695 (m-30) REVERT: B 941 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9091 (mp) REVERT: B 1140 LYS cc_start: 0.9394 (tppp) cc_final: 0.9161 (tmtt) REVERT: B 1146 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8124 (tm-30) REVERT: C 430 MET cc_start: 0.9086 (tpt) cc_final: 0.8866 (tpp) REVERT: C 431 ASP cc_start: 0.8836 (t0) cc_final: 0.8291 (t0) REVERT: C 868 ASP cc_start: 0.8425 (m-30) cc_final: 0.7701 (m-30) REVERT: C 941 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9087 (mp) REVERT: C 984 ASP cc_start: 0.9065 (t0) cc_final: 0.8671 (t0) REVERT: C 1140 LYS cc_start: 0.9394 (tppp) cc_final: 0.9157 (tmtt) REVERT: C 1146 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 1153 GLN cc_start: 0.9481 (pt0) cc_final: 0.9233 (pp30) REVERT: D 430 MET cc_start: 0.9075 (tpt) cc_final: 0.8861 (tpp) REVERT: D 431 ASP cc_start: 0.8827 (t0) cc_final: 0.8250 (t0) REVERT: D 868 ASP cc_start: 0.8430 (m-30) cc_final: 0.7710 (m-30) REVERT: D 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9092 (mp) REVERT: D 1140 LYS cc_start: 0.9393 (tppp) cc_final: 0.9159 (tmtt) REVERT: D 1146 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8183 (tm-30) outliers start: 74 outliers final: 69 residues processed: 433 average time/residue: 0.1855 time to fit residues: 133.4533 Evaluate side-chains 434 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 360 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 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 789 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 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 622 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 36 optimal weight: 9.9990 chunk 326 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 360 optimal weight: 0.9980 chunk 329 optimal weight: 0.3980 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 = 0.103260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.071812 restraints weight = 78165.980| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.27 r_work: 0.2851 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30752 Z= 0.143 Angle : 0.538 7.621 42320 Z= 0.268 Chirality : 0.037 0.218 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.420 20.079 4284 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.41 % Allowed : 15.25 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.14), residues: 3832 helix: 2.52 (0.11), residues: 2448 sheet: -0.32 (0.35), residues: 236 loop : -0.61 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 108 TYR 0.011 0.001 TYR B1063 PHE 0.011 0.001 PHE A 627 TRP 0.010 0.001 TRP C1058 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00328 (30752) covalent geometry : angle 0.53791 (42320) hydrogen bonds : bond 0.03820 ( 1892) hydrogen bonds : angle 3.99850 ( 5496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 365 time to evaluate : 1.199 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 TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7638 (tppt) REVERT: A 430 MET cc_start: 0.9107 (tpt) cc_final: 0.8883 (tpp) REVERT: A 431 ASP cc_start: 0.8864 (t0) cc_final: 0.8309 (t0) REVERT: A 644 ARG cc_start: 0.5898 (tpt170) cc_final: 0.2559 (tmm160) REVERT: A 868 ASP cc_start: 0.8439 (m-30) cc_final: 0.7714 (m-30) REVERT: A 941 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9102 (mp) REVERT: A 1146 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 430 MET cc_start: 0.9105 (tpt) cc_final: 0.8880 (tpp) REVERT: B 431 ASP cc_start: 0.8859 (t0) cc_final: 0.8294 (t0) REVERT: B 644 ARG cc_start: 0.5934 (tpt170) cc_final: 0.2516 (tmm160) REVERT: B 868 ASP cc_start: 0.8448 (m-30) cc_final: 0.7727 (m-30) REVERT: B 941 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9075 (mp) REVERT: B 1140 LYS cc_start: 0.9395 (tppp) cc_final: 0.9159 (tmtt) REVERT: B 1146 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 430 MET cc_start: 0.9098 (tpt) cc_final: 0.8869 (tpp) REVERT: C 431 ASP cc_start: 0.8851 (t0) cc_final: 0.8310 (t0) REVERT: C 644 ARG cc_start: 0.5903 (tpt170) cc_final: 0.2554 (tmm160) REVERT: C 868 ASP cc_start: 0.8442 (m-30) cc_final: 0.7717 (m-30) REVERT: C 941 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 1140 LYS cc_start: 0.9390 (tppp) cc_final: 0.9147 (tmtt) REVERT: C 1146 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 1153 GLN cc_start: 0.9486 (pt0) cc_final: 0.9241 (pp30) REVERT: D 430 MET cc_start: 0.9087 (tpt) cc_final: 0.8860 (tpp) REVERT: D 431 ASP cc_start: 0.8859 (t0) cc_final: 0.8297 (t0) REVERT: D 644 ARG cc_start: 0.5907 (tpt170) cc_final: 0.2562 (tmm160) REVERT: D 868 ASP cc_start: 0.8449 (m-30) cc_final: 0.7727 (m-30) REVERT: D 941 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9104 (mp) REVERT: D 1140 LYS cc_start: 0.9390 (tppp) cc_final: 0.9150 (tmtt) REVERT: D 1146 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8071 (tm-30) outliers start: 71 outliers final: 65 residues processed: 406 average time/residue: 0.1857 time to fit residues: 125.6092 Evaluate side-chains 427 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 981 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 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 622 MET Chi-restraints excluded: chain D residue 636 VAL 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 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 217 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.103674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072821 restraints weight = 79059.763| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.28 r_work: 0.2863 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30752 Z= 0.122 Angle : 0.530 10.361 42320 Z= 0.264 Chirality : 0.037 0.214 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.402 19.274 4284 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.51 % Allowed : 15.22 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3832 helix: 2.52 (0.11), residues: 2448 sheet: -0.32 (0.35), residues: 236 loop : -0.58 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.012 0.001 TYR B 103 PHE 0.012 0.001 PHE A 627 TRP 0.009 0.001 TRP D1058 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00277 (30752) covalent geometry : angle 0.53033 (42320) hydrogen bonds : bond 0.03741 ( 1892) hydrogen bonds : angle 3.97619 ( 5496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6921.29 seconds wall clock time: 119 minutes 22.90 seconds (7162.90 seconds total)