Starting phenix.real_space_refine on Thu Jun 26 00:40:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8y_44362/06_2025/9b8y_44362.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 V 40 8.30 5 S 152 5.16 5 C 19340 2.51 5 N 5232 2.21 5 O 5208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29980 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7455 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 42, 'TRANS': 935} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 399 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' CA': 2, 'DVT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: C, B, D Time building chain proxies: 19.82, per 1000 atoms: 0.66 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: 7.03 Conformation dependent library (CDL) restraints added in 3.4 seconds 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 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: 10.80 Time building geometry restraints manager: 8.33 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 64.840 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30752 Z= 0.209 Angle : 0.475 4.903 42320 Z= 0.261 Chirality : 0.034 0.144 4768 Planarity : 0.003 0.046 5232 Dihedral : 10.411 78.556 10696 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.54 % Allowed : 4.62 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.15), residues: 3832 helix: 2.80 (0.11), residues: 2432 sheet: -0.17 (0.39), residues: 200 loop : -0.63 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1058 HIS 0.005 0.001 HIS A1128 PHE 0.013 0.001 PHE B 931 TYR 0.007 0.001 TYR A1063 ARG 0.002 0.000 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.12248 ( 1892) hydrogen bonds : angle 5.01710 ( 5496) covalent geometry : bond 0.00442 (30752) covalent geometry : angle 0.47491 (42320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 490 time to evaluate : 3.308 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 254 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 332 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8692 (ttm170) REVERT: A 431 ASP cc_start: 0.8518 (t0) cc_final: 0.8207 (t0) REVERT: A 622 MET cc_start: 0.8020 (mtp) cc_final: 0.7782 (mtp) REVERT: B 254 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 332 ARG cc_start: 0.8937 (ttm110) cc_final: 0.8613 (ttm170) REVERT: B 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8227 (t0) REVERT: C 254 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 332 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8592 (ttm170) REVERT: C 431 ASP cc_start: 0.8526 (t0) cc_final: 0.8211 (t0) REVERT: C 1153 GLN cc_start: 0.9281 (pt0) cc_final: 0.9079 (pp30) REVERT: D 254 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 332 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8614 (ttm170) REVERT: D 431 ASP cc_start: 0.8539 (t0) cc_final: 0.8230 (t0) outliers start: 16 outliers final: 0 residues processed: 502 average time/residue: 0.4962 time to fit residues: 396.5557 Evaluate side-chains 330 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN A1017 ASN B 247 ASN B1014 GLN B1017 ASN C 247 ASN C1014 GLN C1017 ASN D 247 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.070512 restraints weight = 79224.401| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.22 r_work: 0.2808 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30752 Z= 0.264 Angle : 0.619 7.527 42320 Z= 0.312 Chirality : 0.040 0.194 4768 Planarity : 0.005 0.047 5232 Dihedral : 3.570 16.249 4284 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.28 % Allowed : 9.51 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3832 helix: 2.47 (0.11), residues: 2452 sheet: 0.15 (0.36), residues: 228 loop : -0.67 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 680 HIS 0.009 0.001 HIS C1128 PHE 0.014 0.001 PHE A 931 TYR 0.016 0.002 TYR A 103 ARG 0.007 0.001 ARG C 857 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 1892) hydrogen bonds : angle 4.43596 ( 5496) covalent geometry : bond 0.00611 (30752) covalent geometry : angle 0.61889 (42320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 6.449 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 254 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 430 MET cc_start: 0.9027 (tpt) cc_final: 0.8787 (tpp) REVERT: A 431 ASP cc_start: 0.8852 (t0) cc_final: 0.8402 (t0) REVERT: A 699 CYS cc_start: 0.8411 (m) cc_final: 0.8184 (t) REVERT: A 868 ASP cc_start: 0.8320 (m-30) cc_final: 0.8057 (m-30) REVERT: A 1146 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 254 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7823 (mt-10) REVERT: B 430 MET cc_start: 0.9046 (tpt) cc_final: 0.8803 (tpp) REVERT: B 431 ASP cc_start: 0.8864 (t0) cc_final: 0.8420 (t0) REVERT: B 670 ASP cc_start: 0.8998 (m-30) cc_final: 0.8515 (m-30) REVERT: B 699 CYS cc_start: 0.8411 (m) cc_final: 0.8182 (t) REVERT: B 868 ASP cc_start: 0.8349 (m-30) cc_final: 0.8086 (m-30) REVERT: B 1146 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 430 MET cc_start: 0.9029 (tpt) cc_final: 0.8785 (tpp) REVERT: C 431 ASP cc_start: 0.8880 (t0) cc_final: 0.8436 (t0) REVERT: C 699 CYS cc_start: 0.8396 (m) cc_final: 0.8164 (t) REVERT: C 868 ASP cc_start: 0.8317 (m-30) cc_final: 0.8058 (m-30) REVERT: C 1146 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 1153 GLN cc_start: 0.9536 (pt0) cc_final: 0.9252 (pp30) REVERT: D 430 MET cc_start: 0.9057 (tpt) cc_final: 0.8811 (tpp) REVERT: D 431 ASP cc_start: 0.8867 (t0) cc_final: 0.8426 (t0) REVERT: D 699 CYS cc_start: 0.8414 (m) cc_final: 0.8186 (t) REVERT: D 868 ASP cc_start: 0.8344 (m-30) cc_final: 0.8080 (m-30) REVERT: D 1146 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8150 (tm-30) outliers start: 67 outliers final: 35 residues processed: 388 average time/residue: 0.4858 time to fit residues: 310.9680 Evaluate side-chains 347 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 930 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 12 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 381 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 242 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 340 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.103411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.072555 restraints weight = 78854.909| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.25 r_work: 0.2856 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30752 Z= 0.129 Angle : 0.530 9.227 42320 Z= 0.266 Chirality : 0.037 0.195 4768 Planarity : 0.004 0.049 5232 Dihedral : 3.537 16.564 4284 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.06 % Allowed : 10.60 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3832 helix: 2.58 (0.11), residues: 2424 sheet: -0.02 (0.36), residues: 236 loop : -0.66 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.007 0.001 HIS D1128 PHE 0.009 0.001 PHE B 80 TYR 0.012 0.001 TYR A1063 ARG 0.004 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1892) hydrogen bonds : angle 4.13355 ( 5496) covalent geometry : bond 0.00289 (30752) covalent geometry : angle 0.52974 (42320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 391 time to evaluate : 3.121 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: symmetry clash REVERT: A 125 SER cc_start: 0.8020 (m) cc_final: 0.7236 (p) REVERT: A 254 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7807 (mt-10) REVERT: A 431 ASP cc_start: 0.8804 (t0) cc_final: 0.8383 (t0) REVERT: A 868 ASP cc_start: 0.8373 (m-30) cc_final: 0.8051 (m-30) REVERT: A 941 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9120 (mp) REVERT: A 1146 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 254 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 431 ASP cc_start: 0.8840 (t0) cc_final: 0.8430 (t0) REVERT: B 868 ASP cc_start: 0.8368 (m-30) cc_final: 0.8050 (m-30) REVERT: B 941 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9115 (mp) REVERT: B 1146 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 431 ASP cc_start: 0.8848 (t0) cc_final: 0.8438 (t0) REVERT: C 868 ASP cc_start: 0.8371 (m-30) cc_final: 0.8052 (m-30) REVERT: C 941 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9125 (mp) REVERT: C 1146 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 1153 GLN cc_start: 0.9525 (pt0) cc_final: 0.9241 (pp30) REVERT: D 431 ASP cc_start: 0.8838 (t0) cc_final: 0.8429 (t0) REVERT: D 868 ASP cc_start: 0.8378 (m-30) cc_final: 0.8058 (m-30) REVERT: D 941 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9118 (mp) REVERT: D 1146 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8168 (tm-30) outliers start: 90 outliers final: 60 residues processed: 442 average time/residue: 0.4619 time to fit residues: 339.0219 Evaluate side-chains 409 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 345 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 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 240 HIS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 134 optimal weight: 0.0870 chunk 123 optimal weight: 7.9990 chunk 252 optimal weight: 6.9990 chunk 379 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 325 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.103499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072828 restraints weight = 78852.839| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.23 r_work: 0.2861 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1935 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= 0.124 Angle : 0.517 8.513 42320 Z= 0.259 Chirality : 0.037 0.136 4768 Planarity : 0.004 0.050 5232 Dihedral : 3.516 20.965 4284 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.40 % Allowed : 11.75 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.14), residues: 3832 helix: 2.53 (0.11), residues: 2444 sheet: -0.42 (0.33), residues: 260 loop : -0.64 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1058 HIS 0.006 0.001 HIS A1128 PHE 0.013 0.001 PHE B 232 TYR 0.011 0.001 TYR A1063 ARG 0.006 0.000 ARG D1136 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1892) hydrogen bonds : angle 4.08135 ( 5496) covalent geometry : bond 0.00280 (30752) covalent geometry : angle 0.51708 (42320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 370 time to evaluate : 3.197 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 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 431 ASP cc_start: 0.8807 (t0) cc_final: 0.8366 (t0) REVERT: A 804 ASP cc_start: 0.9002 (t0) cc_final: 0.8723 (m-30) REVERT: A 868 ASP cc_start: 0.8372 (m-30) cc_final: 0.7981 (m-30) REVERT: A 941 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 1146 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 125 SER cc_start: 0.7966 (m) cc_final: 0.7181 (p) REVERT: B 431 ASP cc_start: 0.8840 (t0) cc_final: 0.8415 (t0) REVERT: B 868 ASP cc_start: 0.8391 (m-30) cc_final: 0.8001 (m-30) REVERT: B 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9105 (mp) REVERT: B 1146 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 1149 LYS cc_start: 0.9108 (tppt) cc_final: 0.8816 (tppt) REVERT: C 431 ASP cc_start: 0.8842 (t0) cc_final: 0.8424 (t0) REVERT: C 868 ASP cc_start: 0.8376 (m-30) cc_final: 0.7984 (m-30) REVERT: C 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9117 (mp) REVERT: C 1140 LYS cc_start: 0.9322 (tmtt) cc_final: 0.9072 (tmtt) REVERT: C 1146 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 1149 LYS cc_start: 0.9100 (tppt) cc_final: 0.8829 (tppt) REVERT: C 1153 GLN cc_start: 0.9502 (pt0) cc_final: 0.9210 (pp30) REVERT: D 431 ASP cc_start: 0.8826 (t0) cc_final: 0.8401 (t0) REVERT: D 868 ASP cc_start: 0.8395 (m-30) cc_final: 0.8007 (m-30) REVERT: D 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9106 (mp) REVERT: D 1134 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9225 (tt) REVERT: D 1146 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 100 outliers final: 68 residues processed: 441 average time/residue: 0.3805 time to fit residues: 278.1467 Evaluate side-chains 419 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 346 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 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 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 858 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 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 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 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 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 1134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 319 optimal weight: 20.0000 chunk 260 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 212 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 1 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073358 restraints weight = 78020.599| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.26 r_work: 0.2886 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 30752 Z= 0.105 Angle : 0.505 7.377 42320 Z= 0.252 Chirality : 0.036 0.183 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.465 20.215 4284 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.55 % Allowed : 12.84 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.14), residues: 3832 helix: 2.56 (0.11), residues: 2440 sheet: -0.24 (0.35), residues: 236 loop : -0.72 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1058 HIS 0.006 0.001 HIS D1128 PHE 0.009 0.001 PHE B 627 TYR 0.011 0.001 TYR A1063 ARG 0.007 0.000 ARG D1136 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 1892) hydrogen bonds : angle 3.99059 ( 5496) covalent geometry : bond 0.00225 (30752) covalent geometry : angle 0.50510 (42320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 387 time to evaluate : 5.498 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 431 ASP cc_start: 0.8808 (t0) cc_final: 0.8340 (t0) REVERT: A 804 ASP cc_start: 0.8989 (t0) cc_final: 0.8685 (m-30) REVERT: A 868 ASP cc_start: 0.8424 (m-30) cc_final: 0.8034 (m-30) REVERT: A 941 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9099 (mp) REVERT: A 1125 GLU cc_start: 0.9393 (tt0) cc_final: 0.9172 (tt0) REVERT: A 1146 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 431 ASP cc_start: 0.8815 (t0) cc_final: 0.8364 (t0) REVERT: B 804 ASP cc_start: 0.8990 (t0) cc_final: 0.8679 (m-30) REVERT: B 868 ASP cc_start: 0.8426 (m-30) cc_final: 0.8036 (m-30) REVERT: B 941 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 984 ASP cc_start: 0.9042 (t0) cc_final: 0.8756 (t0) REVERT: B 1146 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 431 ASP cc_start: 0.8827 (t0) cc_final: 0.8377 (t0) REVERT: C 804 ASP cc_start: 0.8979 (t0) cc_final: 0.8669 (m-30) REVERT: C 868 ASP cc_start: 0.8431 (m-30) cc_final: 0.8041 (m-30) REVERT: C 941 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9101 (mp) REVERT: C 984 ASP cc_start: 0.9043 (t0) cc_final: 0.8755 (t0) REVERT: C 1146 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8270 (tm-30) REVERT: C 1153 GLN cc_start: 0.9502 (pt0) cc_final: 0.9217 (pp30) REVERT: D 431 ASP cc_start: 0.8808 (t0) cc_final: 0.8356 (t0) REVERT: D 804 ASP cc_start: 0.8990 (t0) cc_final: 0.8680 (m-30) REVERT: D 868 ASP cc_start: 0.8421 (m-30) cc_final: 0.8031 (m-30) REVERT: D 941 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9086 (mp) REVERT: D 984 ASP cc_start: 0.9053 (t0) cc_final: 0.8764 (t0) REVERT: D 1146 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8261 (tm-30) outliers start: 75 outliers final: 52 residues processed: 436 average time/residue: 0.4106 time to fit residues: 302.4498 Evaluate side-chains 416 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 360 time to evaluate : 3.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 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 581 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 B residue 105 LEU Chi-restraints excluded: chain B residue 155 THR 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 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 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 275 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 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 823 THR 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 275 LEU 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 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 365 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 157 optimal weight: 0.0770 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073006 restraints weight = 78358.405| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.23 r_work: 0.2868 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30752 Z= 0.133 Angle : 0.506 8.348 42320 Z= 0.254 Chirality : 0.037 0.241 4768 Planarity : 0.004 0.047 5232 Dihedral : 3.468 20.497 4284 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.85 % Allowed : 13.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.14), residues: 3832 helix: 2.56 (0.11), residues: 2444 sheet: -0.30 (0.35), residues: 236 loop : -0.69 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.006 0.001 HIS A1128 PHE 0.013 0.001 PHE C 627 TYR 0.010 0.001 TYR A1063 ARG 0.007 0.000 ARG B1136 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1892) hydrogen bonds : angle 3.97897 ( 5496) covalent geometry : bond 0.00303 (30752) covalent geometry : angle 0.50570 (42320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 365 time to evaluate : 3.397 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. REVERT: A 86 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7609 (tppt) REVERT: A 430 MET cc_start: 0.9094 (tpt) cc_final: 0.8851 (tpt) REVERT: A 431 ASP cc_start: 0.8849 (t0) cc_final: 0.8359 (t0) REVERT: A 804 ASP cc_start: 0.8986 (t0) cc_final: 0.8684 (m-30) REVERT: A 868 ASP cc_start: 0.8464 (m-30) cc_final: 0.7716 (m-30) REVERT: A 941 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 1146 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 86 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7574 (tppt) REVERT: B 430 MET cc_start: 0.9088 (tpt) cc_final: 0.8839 (tpt) REVERT: B 431 ASP cc_start: 0.8847 (t0) cc_final: 0.8339 (t0) REVERT: B 868 ASP cc_start: 0.8459 (m-30) cc_final: 0.7713 (m-30) REVERT: B 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9090 (mp) REVERT: B 1146 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 430 MET cc_start: 0.9108 (tpt) cc_final: 0.8855 (tpt) REVERT: C 431 ASP cc_start: 0.8858 (t0) cc_final: 0.8371 (t0) REVERT: C 868 ASP cc_start: 0.8463 (m-30) cc_final: 0.7719 (m-30) REVERT: C 941 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9098 (mp) REVERT: C 1140 LYS cc_start: 0.9266 (tmtt) cc_final: 0.9027 (tmtt) REVERT: C 1146 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 1153 GLN cc_start: 0.9498 (pt0) cc_final: 0.9228 (pp30) REVERT: D 430 MET cc_start: 0.9103 (tpt) cc_final: 0.8852 (tpt) REVERT: D 431 ASP cc_start: 0.8841 (t0) cc_final: 0.8336 (t0) REVERT: D 868 ASP cc_start: 0.8456 (m-30) cc_final: 0.7709 (m-30) REVERT: D 941 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9095 (mp) REVERT: D 1146 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8282 (tm-30) outliers start: 84 outliers final: 60 residues processed: 416 average time/residue: 0.3595 time to fit residues: 249.0343 Evaluate side-chains 421 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 3.040 ------------------------------------------------------------------------------- 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 155 THR 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 833 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 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 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 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 823 THR Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 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 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 107 optimal weight: 20.0000 chunk 313 optimal weight: 7.9990 chunk 308 optimal weight: 0.0870 chunk 118 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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** ** 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 = 0.3684 r_free = 0.3684 target = 0.104736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.073720 restraints weight = 77439.966| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.23 r_work: 0.2894 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30752 Z= 0.105 Angle : 0.500 8.717 42320 Z= 0.250 Chirality : 0.036 0.249 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.432 19.811 4284 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.55 % Allowed : 14.03 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3832 helix: 2.59 (0.11), residues: 2440 sheet: -0.25 (0.35), residues: 236 loop : -0.68 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1058 HIS 0.005 0.001 HIS C1128 PHE 0.011 0.001 PHE A 627 TYR 0.011 0.001 TYR A1063 ARG 0.011 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1892) hydrogen bonds : angle 3.91502 ( 5496) covalent geometry : bond 0.00231 (30752) covalent geometry : angle 0.50012 (42320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 401 time to evaluate : 2.871 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 TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7590 (tppt) REVERT: A 430 MET cc_start: 0.9084 (tpt) cc_final: 0.8873 (tpt) REVERT: A 431 ASP cc_start: 0.8844 (t0) cc_final: 0.8325 (t0) REVERT: A 868 ASP cc_start: 0.8447 (m-30) cc_final: 0.7741 (m-30) REVERT: A 941 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 1146 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 86 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7556 (tppt) REVERT: B 430 MET cc_start: 0.9095 (tpt) cc_final: 0.8851 (tpt) REVERT: B 431 ASP cc_start: 0.8850 (t0) cc_final: 0.8322 (t0) REVERT: B 644 ARG cc_start: 0.5871 (tpt170) cc_final: 0.3302 (mmm-85) REVERT: B 868 ASP cc_start: 0.8442 (m-30) cc_final: 0.7735 (m-30) REVERT: B 941 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9115 (mp) REVERT: B 984 ASP cc_start: 0.9029 (t0) cc_final: 0.8697 (t0) REVERT: B 1140 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9076 (tmtt) REVERT: B 1146 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 430 MET cc_start: 0.9097 (tpt) cc_final: 0.8853 (tpt) REVERT: C 431 ASP cc_start: 0.8848 (t0) cc_final: 0.8322 (t0) REVERT: C 868 ASP cc_start: 0.8442 (m-30) cc_final: 0.7740 (m-30) REVERT: C 941 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9118 (mp) REVERT: C 984 ASP cc_start: 0.9033 (t0) cc_final: 0.8698 (t0) REVERT: C 1140 LYS cc_start: 0.9296 (tmtt) cc_final: 0.9035 (tmtt) REVERT: C 1146 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 1153 GLN cc_start: 0.9483 (pt0) cc_final: 0.9216 (pp30) REVERT: D 430 MET cc_start: 0.9095 (tpt) cc_final: 0.8854 (tpt) REVERT: D 431 ASP cc_start: 0.8834 (t0) cc_final: 0.8306 (t0) REVERT: D 644 ARG cc_start: 0.5856 (tpt170) cc_final: 0.3329 (mmm-85) REVERT: D 868 ASP cc_start: 0.8438 (m-30) cc_final: 0.7730 (m-30) REVERT: D 941 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9118 (mp) REVERT: D 984 ASP cc_start: 0.9038 (t0) cc_final: 0.8700 (t0) REVERT: D 1140 LYS cc_start: 0.9282 (tmtt) cc_final: 0.9059 (tmtt) REVERT: D 1146 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8292 (tm-30) outliers start: 75 outliers final: 52 residues processed: 451 average time/residue: 0.3827 time to fit residues: 288.2058 Evaluate side-chains 434 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 3.535 ------------------------------------------------------------------------------- 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 296 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 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 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 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 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 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 823 THR 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 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 328 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 304 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.072817 restraints weight = 79042.733| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.29 r_work: 0.2864 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30752 Z= 0.137 Angle : 0.510 8.439 42320 Z= 0.255 Chirality : 0.037 0.238 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.413 20.313 4284 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.89 % Allowed : 14.06 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.14), residues: 3832 helix: 2.58 (0.11), residues: 2444 sheet: -0.33 (0.35), residues: 236 loop : -0.63 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.006 0.001 HIS D1128 PHE 0.012 0.001 PHE D 627 TYR 0.010 0.001 TYR A1063 ARG 0.007 0.000 ARG D1136 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1892) hydrogen bonds : angle 3.94538 ( 5496) covalent geometry : bond 0.00317 (30752) covalent geometry : angle 0.51003 (42320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 365 time to evaluate : 3.286 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7625 (tppt) REVERT: A 431 ASP cc_start: 0.8876 (t0) cc_final: 0.8375 (t0) REVERT: A 804 ASP cc_start: 0.8991 (t0) cc_final: 0.8673 (m-30) REVERT: A 868 ASP cc_start: 0.8433 (m-30) cc_final: 0.7705 (m-30) REVERT: A 941 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9084 (mp) REVERT: A 1146 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8188 (tm-30) REVERT: B 86 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7599 (tppt) REVERT: B 430 MET cc_start: 0.9130 (tpt) cc_final: 0.8901 (tpt) REVERT: B 431 ASP cc_start: 0.8866 (t0) cc_final: 0.8356 (t0) REVERT: B 644 ARG cc_start: 0.5919 (tpt170) cc_final: 0.3386 (mmm-85) REVERT: B 868 ASP cc_start: 0.8438 (m-30) cc_final: 0.7711 (m-30) REVERT: B 941 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9087 (mp) REVERT: B 1146 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 430 MET cc_start: 0.9112 (tpt) cc_final: 0.8881 (tpt) REVERT: C 431 ASP cc_start: 0.8873 (t0) cc_final: 0.8382 (t0) REVERT: C 644 ARG cc_start: 0.5904 (tpt170) cc_final: 0.3401 (mmm-85) REVERT: C 868 ASP cc_start: 0.8462 (m-30) cc_final: 0.7732 (m-30) REVERT: C 941 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9088 (mp) REVERT: C 1140 LYS cc_start: 0.9296 (tmtt) cc_final: 0.9041 (tmtt) REVERT: C 1146 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 1153 GLN cc_start: 0.9486 (pt0) cc_final: 0.9226 (pp30) REVERT: D 430 MET cc_start: 0.9122 (tpt) cc_final: 0.8897 (tpt) REVERT: D 431 ASP cc_start: 0.8865 (t0) cc_final: 0.8360 (t0) REVERT: D 644 ARG cc_start: 0.5886 (tpt170) cc_final: 0.3383 (mmm-85) REVERT: D 868 ASP cc_start: 0.8447 (m-30) cc_final: 0.7721 (m-30) REVERT: D 941 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9105 (mp) REVERT: D 1140 LYS cc_start: 0.9277 (tmtt) cc_final: 0.9031 (tmtt) REVERT: D 1146 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8157 (tm-30) outliers start: 85 outliers final: 68 residues processed: 415 average time/residue: 0.3793 time to fit residues: 262.3023 Evaluate side-chains 430 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 356 time to evaluate : 3.325 ------------------------------------------------------------------------------- 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 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 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 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 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 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 163 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.103508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072052 restraints weight = 78255.272| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.28 r_work: 0.2858 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30752 Z= 0.142 Angle : 0.520 8.733 42320 Z= 0.260 Chirality : 0.037 0.210 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.403 19.983 4284 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.65 % Allowed : 14.50 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3832 helix: 2.57 (0.11), residues: 2448 sheet: -0.42 (0.34), residues: 236 loop : -0.61 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1058 HIS 0.006 0.001 HIS A1128 PHE 0.011 0.001 PHE D 627 TYR 0.010 0.001 TYR D1063 ARG 0.008 0.000 ARG B1136 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1892) hydrogen bonds : angle 3.94973 ( 5496) covalent geometry : bond 0.00328 (30752) covalent geometry : angle 0.51997 (42320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 3.376 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7643 (tppt) REVERT: A 431 ASP cc_start: 0.8733 (t0) cc_final: 0.8185 (t0) REVERT: A 644 ARG cc_start: 0.5881 (tpt170) cc_final: 0.3357 (mmm-85) REVERT: A 868 ASP cc_start: 0.8434 (m-30) cc_final: 0.7712 (m-30) REVERT: A 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9098 (mp) REVERT: A 1146 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 86 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7632 (tppt) REVERT: B 430 MET cc_start: 0.9136 (tpt) cc_final: 0.8935 (tpt) REVERT: B 431 ASP cc_start: 0.8873 (t0) cc_final: 0.8366 (t0) REVERT: B 644 ARG cc_start: 0.5908 (tpt170) cc_final: 0.3330 (mmm-85) REVERT: B 868 ASP cc_start: 0.8432 (m-30) cc_final: 0.7707 (m-30) REVERT: B 941 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9083 (mp) REVERT: B 1140 LYS cc_start: 0.9275 (tmtt) cc_final: 0.9055 (tmtt) REVERT: B 1146 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 431 ASP cc_start: 0.8871 (t0) cc_final: 0.8370 (t0) REVERT: C 644 ARG cc_start: 0.5918 (tpt170) cc_final: 0.3379 (mmm-85) REVERT: C 868 ASP cc_start: 0.8444 (m-30) cc_final: 0.7724 (m-30) REVERT: C 941 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9091 (mp) REVERT: C 1140 LYS cc_start: 0.9297 (tmtt) cc_final: 0.9025 (tmtt) REVERT: C 1146 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 1153 GLN cc_start: 0.9478 (pt0) cc_final: 0.9226 (pp30) REVERT: D 431 ASP cc_start: 0.8867 (t0) cc_final: 0.8364 (t0) REVERT: D 644 ARG cc_start: 0.5912 (tpt170) cc_final: 0.3371 (mmm-85) REVERT: D 868 ASP cc_start: 0.8448 (m-30) cc_final: 0.7728 (m-30) REVERT: D 941 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9077 (mp) REVERT: D 1146 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8197 (tm-30) outliers start: 78 outliers final: 72 residues processed: 405 average time/residue: 0.3799 time to fit residues: 257.8324 Evaluate side-chains 428 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 350 time to evaluate : 3.384 ------------------------------------------------------------------------------- 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 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 823 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 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 137 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 440 PHE Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 858 LEU Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 100 optimal weight: 0.7980 chunk 199 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.073668 restraints weight = 78597.145| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.29 r_work: 0.2882 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30752 Z= 0.110 Angle : 0.518 8.860 42320 Z= 0.256 Chirality : 0.036 0.203 4768 Planarity : 0.004 0.046 5232 Dihedral : 3.396 19.183 4284 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.14), residues: 3832 helix: 2.55 (0.11), residues: 2444 sheet: -0.31 (0.35), residues: 236 loop : -0.60 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C1058 HIS 0.005 0.001 HIS D1128 PHE 0.011 0.001 PHE D 627 TYR 0.011 0.001 TYR A1063 ARG 0.008 0.000 ARG D1136 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 1892) hydrogen bonds : angle 3.92727 ( 5496) covalent geometry : bond 0.00247 (30752) covalent geometry : angle 0.51817 (42320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7664 Ramachandran restraints generated. 3832 Oldfield, 0 Emsley, 3832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 360 time to evaluate : 6.270 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU A 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU B 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU C 413 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU D 413 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7616 (tppt) REVERT: A 431 ASP cc_start: 0.8650 (t0) cc_final: 0.8109 (t0) REVERT: A 644 ARG cc_start: 0.5894 (tpt170) cc_final: 0.3341 (mmm-85) REVERT: A 804 ASP cc_start: 0.8984 (t0) cc_final: 0.8663 (m-30) REVERT: A 868 ASP cc_start: 0.8431 (m-30) cc_final: 0.7698 (m-30) REVERT: A 941 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9097 (mp) REVERT: A 1146 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 86 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7610 (tppt) REVERT: B 430 MET cc_start: 0.9136 (tpt) cc_final: 0.8930 (tpt) REVERT: B 431 ASP cc_start: 0.8859 (t0) cc_final: 0.8350 (t0) REVERT: B 622 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8849 (mtp) REVERT: B 644 ARG cc_start: 0.5895 (tpt170) cc_final: 0.3320 (mmm-85) REVERT: B 868 ASP cc_start: 0.8425 (m-30) cc_final: 0.7692 (m-30) REVERT: B 941 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9091 (mp) REVERT: B 1146 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 431 ASP cc_start: 0.8686 (t0) cc_final: 0.8126 (t0) REVERT: C 644 ARG cc_start: 0.5879 (tpt170) cc_final: 0.3340 (mmm-85) REVERT: C 868 ASP cc_start: 0.8442 (m-30) cc_final: 0.7715 (m-30) REVERT: C 941 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9102 (mp) REVERT: C 1140 LYS cc_start: 0.9313 (tmtt) cc_final: 0.9035 (tmtt) REVERT: C 1146 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 1153 GLN cc_start: 0.9473 (pt0) cc_final: 0.9229 (pp30) REVERT: D 431 ASP cc_start: 0.8680 (t0) cc_final: 0.8121 (t0) REVERT: D 622 MET cc_start: 0.9087 (mtp) cc_final: 0.8839 (mtp) REVERT: D 644 ARG cc_start: 0.5892 (tpt170) cc_final: 0.3351 (mmm-85) REVERT: D 868 ASP cc_start: 0.8443 (m-30) cc_final: 0.7712 (m-30) REVERT: D 941 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9106 (mp) REVERT: D 1140 LYS cc_start: 0.9280 (tmtt) cc_final: 0.9062 (tmtt) REVERT: D 1146 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8124 (tm-30) outliers start: 75 outliers final: 68 residues processed: 408 average time/residue: 0.5303 time to fit residues: 365.6180 Evaluate side-chains 427 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 352 time to evaluate : 6.508 ------------------------------------------------------------------------------- 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 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 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 86 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 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 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 823 THR 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 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 823 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 930 VAL Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 981 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 440 PHE Chi-restraints excluded: chain D residue 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 877 LEU Chi-restraints excluded: chain D residue 930 VAL Chi-restraints excluded: chain D residue 941 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 164 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 209 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 375 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 chunk 335 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.071800 restraints weight = 78393.854| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.29 r_work: 0.2850 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30752 Z= 0.154 Angle : 0.536 8.339 42320 Z= 0.267 Chirality : 0.037 0.208 4768 Planarity : 0.004 0.048 5232 Dihedral : 3.391 19.780 4284 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.68 % Allowed : 14.84 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.14), residues: 3832 helix: 2.55 (0.11), residues: 2448 sheet: -0.38 (0.34), residues: 236 loop : -0.56 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.005 0.001 HIS C1128 PHE 0.012 0.001 PHE D 627 TYR 0.010 0.001 TYR A1063 ARG 0.004 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1892) hydrogen bonds : angle 3.97392 ( 5496) covalent geometry : bond 0.00357 (30752) covalent geometry : angle 0.53567 (42320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17831.38 seconds wall clock time: 318 minutes 52.42 seconds (19132.42 seconds total)