Starting phenix.real_space_refine on Sat Mar 7 04:59:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.map" model { file = "/net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vtp_32119/03_2026/7vtp_32119.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 336 5.16 5 C 24486 2.51 5 N 6468 2.21 5 O 7056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38358 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 6338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6338 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 772} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'7YN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.98, per 1000 atoms: 0.21 Number of scatterers: 38358 At special positions: 0 Unit cell: (158.115, 163.095, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 336 16.00 P 12 15.00 O 7056 8.00 N 6468 7.00 C 24486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9048 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 29 sheets defined 54.9% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 231 through 246 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.719A pdb=" N PHE A 386 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 401 removed outlier: 3.646A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 438 through 451 Processing helix chain 'A' and resid 463 through 480 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.530A pdb=" N VAL A 499 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.597A pdb=" N GLN A 526 " --> pdb=" O HIS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.702A pdb=" N LEU A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 587 through 597 removed outlier: 3.638A pdb=" N TYR A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 3.766A pdb=" N LEU A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 639 through 647 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 659 through 673 Processing helix chain 'A' and resid 727 through 740 removed outlier: 4.484A pdb=" N GLY A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 735 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 766 Processing helix chain 'A' and resid 783 through 797 removed outlier: 3.978A pdb=" N CYS A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 788 " --> pdb=" O HIS A 784 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.763A pdb=" N VAL A 820 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.695A pdb=" N SER A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 880 removed outlier: 3.568A pdb=" N GLY A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 924 through 937 removed outlier: 3.648A pdb=" N GLY A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 968 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'B' and resid 271 through 280 Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.756A pdb=" N PHE B 386 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 401 removed outlier: 3.936A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 438 through 451 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 485 through 492 removed outlier: 3.506A pdb=" N HIS B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 499 Processing helix chain 'B' and resid 522 through 536 removed outlier: 3.665A pdb=" N GLN B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.735A pdb=" N LEU B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 Processing helix chain 'B' and resid 587 through 597 Processing helix chain 'B' and resid 602 through 618 removed outlier: 3.781A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 638 Processing helix chain 'B' and resid 639 through 647 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 659 through 673 Processing helix chain 'B' and resid 727 through 740 removed outlier: 4.366A pdb=" N GLY B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 736 " --> pdb=" O GLY B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 766 Processing helix chain 'B' and resid 783 through 797 removed outlier: 4.024A pdb=" N CYS B 787 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 788 " --> pdb=" O HIS B 784 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 823 removed outlier: 3.783A pdb=" N VAL B 820 " --> pdb=" O ARG B 816 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.651A pdb=" N SER B 849 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 880 removed outlier: 3.549A pdb=" N GLY B 871 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 911 Processing helix chain 'B' and resid 924 through 937 removed outlier: 3.682A pdb=" N GLY B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 956 No H-bonds generated for 'chain 'B' and resid 954 through 956' Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 982 through 994 Processing helix chain 'B' and resid 1011 through 1025 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 286 through 292 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 351 through 360 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.737A pdb=" N PHE C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 401 removed outlier: 3.713A pdb=" N GLU C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 438 through 451 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 495 through 499 Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.652A pdb=" N GLN C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 564 removed outlier: 3.706A pdb=" N LEU C 561 " --> pdb=" O ASP C 557 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 564 " --> pdb=" O VAL C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 584 Processing helix chain 'C' and resid 587 through 597 removed outlier: 3.560A pdb=" N TYR C 591 " --> pdb=" O GLU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 618 removed outlier: 3.771A pdb=" N LEU C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 638 Processing helix chain 'C' and resid 639 through 647 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 659 through 673 Processing helix chain 'C' and resid 727 through 740 removed outlier: 4.202A pdb=" N GLY C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER C 735 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 766 Processing helix chain 'C' and resid 783 through 797 removed outlier: 3.991A pdb=" N CYS C 787 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE C 788 " --> pdb=" O HIS C 784 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP C 789 " --> pdb=" O GLU C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 823 removed outlier: 3.775A pdb=" N VAL C 820 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 removed outlier: 3.709A pdb=" N SER C 849 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 880 removed outlier: 3.534A pdb=" N GLY C 871 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 911 Processing helix chain 'C' and resid 924 through 937 removed outlier: 3.729A pdb=" N GLY C 928 " --> pdb=" O LEU C 924 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 956 No H-bonds generated for 'chain 'C' and resid 954 through 956' Processing helix chain 'C' and resid 957 through 968 removed outlier: 3.555A pdb=" N SER C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 Processing helix chain 'C' and resid 1011 through 1025 Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 231 through 246 Processing helix chain 'D' and resid 271 through 280 Processing helix chain 'D' and resid 286 through 292 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.719A pdb=" N PHE D 386 " --> pdb=" O PHE D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 401 removed outlier: 3.645A pdb=" N GLU D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 411 through 428 Processing helix chain 'D' and resid 438 through 451 Processing helix chain 'D' and resid 463 through 480 Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 495 through 499 removed outlier: 3.530A pdb=" N VAL D 499 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.597A pdb=" N GLN D 526 " --> pdb=" O HIS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 564 removed outlier: 3.702A pdb=" N LEU D 561 " --> pdb=" O ASP D 557 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 Processing helix chain 'D' and resid 587 through 597 removed outlier: 3.638A pdb=" N TYR D 591 " --> pdb=" O GLU D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 618 removed outlier: 3.766A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 638 Processing helix chain 'D' and resid 639 through 647 Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 659 through 673 Processing helix chain 'D' and resid 727 through 740 removed outlier: 4.485A pdb=" N GLY D 732 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 735 " --> pdb=" O ARG D 731 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 766 Processing helix chain 'D' and resid 783 through 797 removed outlier: 3.979A pdb=" N CYS D 787 " --> pdb=" O SER D 783 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE D 788 " --> pdb=" O HIS D 784 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 823 removed outlier: 3.763A pdb=" N VAL D 820 " --> pdb=" O ARG D 816 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY D 821 " --> pdb=" O LEU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 852 removed outlier: 3.695A pdb=" N SER D 849 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 880 removed outlier: 3.569A pdb=" N GLY D 871 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 911 Processing helix chain 'D' and resid 924 through 937 removed outlier: 3.647A pdb=" N GLY D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 956 No H-bonds generated for 'chain 'D' and resid 954 through 956' Processing helix chain 'D' and resid 957 through 968 Processing helix chain 'D' and resid 982 through 994 Processing helix chain 'D' and resid 1011 through 1025 Processing helix chain 'E' and resid 136 through 148 Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 204 through 210 Processing helix chain 'E' and resid 231 through 246 Processing helix chain 'E' and resid 271 through 280 Processing helix chain 'E' and resid 286 through 292 Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 351 through 360 Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.770A pdb=" N PHE E 386 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 401 removed outlier: 3.954A pdb=" N GLU E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 411 through 428 Processing helix chain 'E' and resid 438 through 451 Processing helix chain 'E' and resid 463 through 480 Processing helix chain 'E' and resid 485 through 492 removed outlier: 3.515A pdb=" N HIS E 492 " --> pdb=" O ASP E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'E' and resid 522 through 536 removed outlier: 3.665A pdb=" N GLN E 526 " --> pdb=" O HIS E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 564 removed outlier: 3.722A pdb=" N LEU E 561 " --> pdb=" O ASP E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 568 through 584 Processing helix chain 'E' and resid 587 through 597 Processing helix chain 'E' and resid 602 through 618 removed outlier: 3.767A pdb=" N LEU E 606 " --> pdb=" O GLN E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 638 Processing helix chain 'E' and resid 639 through 647 Processing helix chain 'E' and resid 648 through 650 No H-bonds generated for 'chain 'E' and resid 648 through 650' Processing helix chain 'E' and resid 659 through 673 Processing helix chain 'E' and resid 727 through 740 removed outlier: 4.346A pdb=" N GLY E 732 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 735 " --> pdb=" O ARG E 731 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 736 " --> pdb=" O GLY E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 766 Processing helix chain 'E' and resid 783 through 797 removed outlier: 4.024A pdb=" N CYS E 787 " --> pdb=" O SER E 783 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE E 788 " --> pdb=" O HIS E 784 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP E 789 " --> pdb=" O GLU E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 810 through 823 removed outlier: 3.778A pdb=" N VAL E 820 " --> pdb=" O ARG E 816 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 843 through 852 removed outlier: 3.653A pdb=" N SER E 849 " --> pdb=" O GLN E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 880 removed outlier: 3.550A pdb=" N GLY E 871 " --> pdb=" O LEU E 867 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 911 Processing helix chain 'E' and resid 924 through 937 removed outlier: 3.672A pdb=" N GLY E 928 " --> pdb=" O LEU E 924 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY E 935 " --> pdb=" O LEU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 956 No H-bonds generated for 'chain 'E' and resid 954 through 956' Processing helix chain 'E' and resid 957 through 968 Processing helix chain 'E' and resid 982 through 994 Processing helix chain 'E' and resid 1011 through 1025 Processing helix chain 'F' and resid 136 through 148 Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 204 through 210 Processing helix chain 'F' and resid 231 through 245 Processing helix chain 'F' and resid 271 through 280 Processing helix chain 'F' and resid 286 through 292 Processing helix chain 'F' and resid 293 through 295 No H-bonds generated for 'chain 'F' and resid 293 through 295' Processing helix chain 'F' and resid 328 through 337 Processing helix chain 'F' and resid 351 through 360 Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.735A pdb=" N PHE F 386 " --> pdb=" O PHE F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 401 removed outlier: 3.716A pdb=" N GLU F 401 " --> pdb=" O SER F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 409 Processing helix chain 'F' and resid 411 through 428 Processing helix chain 'F' and resid 438 through 451 Processing helix chain 'F' and resid 463 through 479 Processing helix chain 'F' and resid 485 through 492 Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'F' and resid 522 through 536 removed outlier: 3.651A pdb=" N GLN F 526 " --> pdb=" O HIS F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.690A pdb=" N LEU F 561 " --> pdb=" O ASP F 557 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 564 " --> pdb=" O VAL F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 584 Processing helix chain 'F' and resid 587 through 597 Processing helix chain 'F' and resid 602 through 618 removed outlier: 3.774A pdb=" N LEU F 606 " --> pdb=" O GLN F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 638 Processing helix chain 'F' and resid 639 through 647 Processing helix chain 'F' and resid 648 through 650 No H-bonds generated for 'chain 'F' and resid 648 through 650' Processing helix chain 'F' and resid 659 through 673 Processing helix chain 'F' and resid 727 through 740 removed outlier: 4.187A pdb=" N GLY F 732 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 735 " --> pdb=" O ARG F 731 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 736 " --> pdb=" O GLY F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 766 Processing helix chain 'F' and resid 783 through 797 removed outlier: 3.995A pdb=" N CYS F 787 " --> pdb=" O SER F 783 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE F 788 " --> pdb=" O HIS F 784 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP F 789 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing helix chain 'F' and resid 810 through 823 removed outlier: 3.774A pdb=" N VAL F 820 " --> pdb=" O ARG F 816 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY F 821 " --> pdb=" O LEU F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 843 through 852 removed outlier: 3.690A pdb=" N SER F 849 " --> pdb=" O GLN F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 867 through 880 removed outlier: 3.570A pdb=" N GLY F 871 " --> pdb=" O LEU F 867 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 900 through 911 Processing helix chain 'F' and resid 924 through 937 removed outlier: 3.727A pdb=" N GLY F 928 " --> pdb=" O LEU F 924 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY F 935 " --> pdb=" O LEU F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 954 through 956 No H-bonds generated for 'chain 'F' and resid 954 through 956' Processing helix chain 'F' and resid 957 through 968 removed outlier: 3.555A pdb=" N SER F 967 " --> pdb=" O THR F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 982 through 994 Processing helix chain 'F' and resid 1011 through 1025 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 5.995A pdb=" N ARG A 172 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 221 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 368 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 223 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 370 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 225 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A 372 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 297 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU A 347 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 299 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N THR A 349 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET A 301 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR A 255 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 300 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 257 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP A 302 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 259 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA4, first strand: chain 'A' and resid 653 through 657 Processing sheet with id=AA5, first strand: chain 'A' and resid 745 through 747 removed outlier: 6.792A pdb=" N LEU A 746 " --> pdb=" O TRP A 776 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU A 775 " --> pdb=" O ASP A 804 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 803 " --> pdb=" O TRP A 833 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU A 889 " --> pdb=" O TYR A 918 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU A 917 " --> pdb=" O GLU A 947 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU A 946 " --> pdb=" O SER A 975 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 974 " --> pdb=" O GLY A1004 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 5.948A pdb=" N ARG B 172 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 221 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL B 368 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 223 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE B 370 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN B 225 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY B 372 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 297 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU B 347 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 299 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR B 349 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET B 301 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR B 255 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU B 300 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 257 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP B 302 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 259 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AA8, first strand: chain 'B' and resid 503 through 506 Processing sheet with id=AA9, first strand: chain 'B' and resid 653 through 657 Processing sheet with id=AB1, first strand: chain 'B' and resid 745 through 747 removed outlier: 6.864A pdb=" N LEU B 746 " --> pdb=" O TRP B 776 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 775 " --> pdb=" O ASP B 804 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU B 803 " --> pdb=" O TRP B 833 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 889 " --> pdb=" O TYR B 918 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 917 " --> pdb=" O GLU B 947 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU B 946 " --> pdb=" O SER B 975 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU B 974 " --> pdb=" O GLY B1004 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 172 through 175 removed outlier: 5.990A pdb=" N ARG C 172 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR C 221 " --> pdb=" O ARG C 366 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL C 368 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 223 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 370 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 225 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY C 372 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE C 297 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU C 347 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE C 299 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR C 349 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET C 301 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR C 255 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 300 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE C 257 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP C 302 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AB4, first strand: chain 'C' and resid 503 through 506 Processing sheet with id=AB5, first strand: chain 'C' and resid 653 through 657 Processing sheet with id=AB6, first strand: chain 'C' and resid 745 through 747 removed outlier: 6.827A pdb=" N LEU C 746 " --> pdb=" O TRP C 776 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU C 775 " --> pdb=" O ASP C 804 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 803 " --> pdb=" O TRP C 833 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 889 " --> pdb=" O TYR C 918 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU C 917 " --> pdb=" O GLU C 947 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C 946 " --> pdb=" O SER C 975 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU C 974 " --> pdb=" O GLY C1004 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 172 through 175 removed outlier: 5.994A pdb=" N ARG D 172 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR D 221 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL D 368 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 223 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 370 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN D 225 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY D 372 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 297 " --> pdb=" O SER D 345 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 347 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE D 299 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR D 349 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N MET D 301 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR D 255 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 300 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE D 257 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP D 302 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE D 259 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AB9, first strand: chain 'D' and resid 504 through 505 Processing sheet with id=AC1, first strand: chain 'D' and resid 653 through 657 Processing sheet with id=AC2, first strand: chain 'D' and resid 745 through 747 removed outlier: 6.792A pdb=" N LEU D 746 " --> pdb=" O TRP D 776 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU D 775 " --> pdb=" O ASP D 804 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU D 803 " --> pdb=" O TRP D 833 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU D 889 " --> pdb=" O TYR D 918 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU D 917 " --> pdb=" O GLU D 947 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU D 946 " --> pdb=" O SER D 975 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 974 " --> pdb=" O GLY D1004 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 172 through 175 removed outlier: 5.957A pdb=" N ARG E 172 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 221 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL E 368 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 223 " --> pdb=" O VAL E 368 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE E 370 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLN E 225 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY E 372 " --> pdb=" O GLN E 225 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE E 297 " --> pdb=" O SER E 345 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU E 347 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE E 299 " --> pdb=" O LEU E 347 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR E 349 " --> pdb=" O PHE E 299 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET E 301 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 255 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 300 " --> pdb=" O TYR E 255 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE E 257 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASP E 302 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 259 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AC5, first strand: chain 'E' and resid 503 through 506 Processing sheet with id=AC6, first strand: chain 'E' and resid 653 through 657 Processing sheet with id=AC7, first strand: chain 'E' and resid 745 through 747 removed outlier: 6.762A pdb=" N LEU E 746 " --> pdb=" O TRP E 776 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU E 775 " --> pdb=" O ASP E 804 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU E 803 " --> pdb=" O TRP E 833 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU E 889 " --> pdb=" O TYR E 918 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU E 917 " --> pdb=" O GLU E 947 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU E 946 " --> pdb=" O SER E 975 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU E 974 " --> pdb=" O GLY E1004 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 172 through 175 removed outlier: 5.989A pdb=" N ARG F 172 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR F 221 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL F 368 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL F 223 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE F 370 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN F 225 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY F 372 " --> pdb=" O GLN F 225 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE F 297 " --> pdb=" O SER F 345 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU F 347 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE F 299 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR F 349 " --> pdb=" O PHE F 299 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET F 301 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR F 255 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 300 " --> pdb=" O TYR F 255 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE F 257 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP F 302 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE F 259 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 269 through 270 Processing sheet with id=AD1, first strand: chain 'F' and resid 503 through 506 Processing sheet with id=AD2, first strand: chain 'F' and resid 653 through 657 removed outlier: 3.533A pdb=" N LEU F 679 " --> pdb=" O GLU F 745 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 746 " --> pdb=" O TRP F 776 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU F 775 " --> pdb=" O ASP F 804 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU F 803 " --> pdb=" O TRP F 833 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 889 " --> pdb=" O TYR F 918 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU F 917 " --> pdb=" O GLU F 947 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU F 946 " --> pdb=" O SER F 975 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU F 974 " --> pdb=" O GLY F1004 " (cutoff:3.500A) 1745 hydrogen bonds defined for protein. 5166 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: 8.74 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12204 1.34 - 1.46: 6649 1.46 - 1.58: 19781 1.58 - 1.69: 19 1.69 - 1.81: 449 Bond restraints: 39102 Sorted by residual: bond pdb=" C08 7YN B1502 " pdb=" C09 7YN B1502 " ideal model delta sigma weight residual 1.340 1.529 -0.189 2.00e-02 2.50e+03 8.91e+01 bond pdb=" C08 7YN A1502 " pdb=" C09 7YN A1502 " ideal model delta sigma weight residual 1.340 1.529 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" C08 7YN D1502 " pdb=" C09 7YN D1502 " ideal model delta sigma weight residual 1.340 1.528 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C08 7YN E1502 " pdb=" C09 7YN E1502 " ideal model delta sigma weight residual 1.340 1.528 -0.188 2.00e-02 2.50e+03 8.83e+01 bond pdb=" C08 7YN F1502 " pdb=" C09 7YN F1502 " ideal model delta sigma weight residual 1.340 1.528 -0.188 2.00e-02 2.50e+03 8.81e+01 ... (remaining 39097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 52558 3.99 - 7.97: 214 7.97 - 11.96: 6 11.96 - 15.95: 0 15.95 - 19.93: 4 Bond angle restraints: 52782 Sorted by residual: angle pdb=" C SER A 216 " pdb=" N GLU A 217 " pdb=" CA GLU A 217 " ideal model delta sigma weight residual 120.68 140.61 -19.93 1.52e+00 4.33e-01 1.72e+02 angle pdb=" C SER D 216 " pdb=" N GLU D 217 " pdb=" CA GLU D 217 " ideal model delta sigma weight residual 120.68 140.61 -19.93 1.52e+00 4.33e-01 1.72e+02 angle pdb=" CA PRO B 218 " pdb=" N PRO B 218 " pdb=" CD PRO B 218 " ideal model delta sigma weight residual 112.00 102.40 9.60 1.40e+00 5.10e-01 4.70e+01 angle pdb=" N PRO B 218 " pdb=" CD PRO B 218 " pdb=" CG PRO B 218 " ideal model delta sigma weight residual 103.20 93.66 9.54 1.50e+00 4.44e-01 4.04e+01 angle pdb=" C GLU A 217 " pdb=" N PRO A 218 " pdb=" CD PRO A 218 " ideal model delta sigma weight residual 125.00 105.19 19.81 4.10e+00 5.95e-02 2.33e+01 ... (remaining 52777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 22807 28.40 - 56.81: 691 56.81 - 85.21: 81 85.21 - 113.61: 10 113.61 - 142.02: 9 Dihedral angle restraints: 23598 sinusoidal: 9684 harmonic: 13914 Sorted by residual: dihedral pdb=" CA PHE E 650 " pdb=" C PHE E 650 " pdb=" N PRO E 651 " pdb=" CA PRO E 651 " ideal model delta harmonic sigma weight residual -180.00 -135.76 -44.24 0 5.00e+00 4.00e-02 7.83e+01 dihedral pdb=" CA PHE A 650 " pdb=" C PHE A 650 " pdb=" N PRO A 651 " pdb=" CA PRO A 651 " ideal model delta harmonic sigma weight residual -180.00 -136.39 -43.61 0 5.00e+00 4.00e-02 7.61e+01 dihedral pdb=" CA PHE D 650 " pdb=" C PHE D 650 " pdb=" N PRO D 651 " pdb=" CA PRO D 651 " ideal model delta harmonic sigma weight residual 180.00 -136.43 -43.57 0 5.00e+00 4.00e-02 7.59e+01 ... (remaining 23595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5258 0.058 - 0.116: 683 0.116 - 0.174: 50 0.174 - 0.232: 7 0.232 - 0.290: 2 Chirality restraints: 6000 Sorted by residual: chirality pdb=" CA PRO D 218 " pdb=" N PRO D 218 " pdb=" C PRO D 218 " pdb=" CB PRO D 218 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA PRO A 218 " pdb=" N PRO A 218 " pdb=" C PRO A 218 " pdb=" CB PRO A 218 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU D 355 " pdb=" CB LEU D 355 " pdb=" CD1 LEU D 355 " pdb=" CD2 LEU D 355 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 5997 not shown) Planarity restraints: 6570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7YN A1502 " -0.033 2.00e-02 2.50e+03 6.63e-02 1.43e+02 pdb=" C02 7YN A1502 " -0.026 2.00e-02 2.50e+03 pdb=" C03 7YN A1502 " -0.041 2.00e-02 2.50e+03 pdb=" C04 7YN A1502 " -0.017 2.00e-02 2.50e+03 pdb=" C05 7YN A1502 " -0.035 2.00e-02 2.50e+03 pdb=" C06 7YN A1502 " -0.022 2.00e-02 2.50e+03 pdb=" C07 7YN A1502 " 0.001 2.00e-02 2.50e+03 pdb=" C08 7YN A1502 " 0.109 2.00e-02 2.50e+03 pdb=" C09 7YN A1502 " -0.013 2.00e-02 2.50e+03 pdb=" C10 7YN A1502 " -0.045 2.00e-02 2.50e+03 pdb=" C11 7YN A1502 " 0.186 2.00e-02 2.50e+03 pdb=" C12 7YN A1502 " -0.054 2.00e-02 2.50e+03 pdb=" N13 7YN A1502 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN D1502 " 0.034 2.00e-02 2.50e+03 6.62e-02 1.42e+02 pdb=" C02 7YN D1502 " 0.026 2.00e-02 2.50e+03 pdb=" C03 7YN D1502 " 0.040 2.00e-02 2.50e+03 pdb=" C04 7YN D1502 " 0.017 2.00e-02 2.50e+03 pdb=" C05 7YN D1502 " 0.035 2.00e-02 2.50e+03 pdb=" C06 7YN D1502 " 0.022 2.00e-02 2.50e+03 pdb=" C07 7YN D1502 " -0.001 2.00e-02 2.50e+03 pdb=" C08 7YN D1502 " -0.109 2.00e-02 2.50e+03 pdb=" C09 7YN D1502 " 0.013 2.00e-02 2.50e+03 pdb=" C10 7YN D1502 " 0.045 2.00e-02 2.50e+03 pdb=" C11 7YN D1502 " -0.185 2.00e-02 2.50e+03 pdb=" C12 7YN D1502 " 0.054 2.00e-02 2.50e+03 pdb=" N13 7YN D1502 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7YN C1502 " -0.033 2.00e-02 2.50e+03 6.05e-02 1.19e+02 pdb=" C02 7YN C1502 " -0.024 2.00e-02 2.50e+03 pdb=" C03 7YN C1502 " -0.040 2.00e-02 2.50e+03 pdb=" C04 7YN C1502 " -0.010 2.00e-02 2.50e+03 pdb=" C05 7YN C1502 " -0.031 2.00e-02 2.50e+03 pdb=" C06 7YN C1502 " -0.014 2.00e-02 2.50e+03 pdb=" C07 7YN C1502 " 0.012 2.00e-02 2.50e+03 pdb=" C08 7YN C1502 " 0.074 2.00e-02 2.50e+03 pdb=" C09 7YN C1502 " -0.000 2.00e-02 2.50e+03 pdb=" C10 7YN C1502 " -0.050 2.00e-02 2.50e+03 pdb=" C11 7YN C1502 " 0.179 2.00e-02 2.50e+03 pdb=" C12 7YN C1502 " -0.056 2.00e-02 2.50e+03 pdb=" N13 7YN C1502 " -0.006 2.00e-02 2.50e+03 ... (remaining 6567 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 526 2.67 - 3.23: 37243 3.23 - 3.78: 59673 3.78 - 4.34: 82065 4.34 - 4.90: 133252 Nonbonded interactions: 312759 Sorted by model distance: nonbonded pdb=" OH TYR C 632 " pdb=" OD1 ASP C 662 " model vdw 2.111 3.040 nonbonded pdb=" OH TYR F 632 " pdb=" OD1 ASP F 662 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR B 632 " pdb=" OD1 ASP B 662 " model vdw 2.135 3.040 nonbonded pdb=" OH TYR E 632 " pdb=" OD1 ASP E 662 " model vdw 2.140 3.040 nonbonded pdb=" OH TYR A 632 " pdb=" OD1 ASP A 662 " model vdw 2.160 3.040 ... (remaining 312754 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.090 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.189 39102 Z= 0.200 Angle : 0.682 19.933 52782 Z= 0.349 Chirality : 0.039 0.290 6000 Planarity : 0.006 0.177 6570 Dihedral : 13.982 142.017 14550 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.69 % Favored : 97.14 % Rotamer: Outliers : 0.09 % Allowed : 0.21 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4686 helix: 0.73 (0.11), residues: 2394 sheet: -1.27 (0.20), residues: 654 loop : 0.19 (0.17), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 605 TYR 0.019 0.001 TYR C1009 PHE 0.014 0.001 PHE B 396 TRP 0.017 0.002 TRP E 322 HIS 0.004 0.001 HIS D 663 Details of bonding type rmsd covalent geometry : bond 0.00416 (39102) covalent geometry : angle 0.68169 (52782) hydrogen bonds : bond 0.17205 ( 1745) hydrogen bonds : angle 6.47602 ( 5166) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 354 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8840 (tpp) cc_final: 0.8627 (tpp) REVERT: B 277 MET cc_start: 0.8498 (mmt) cc_final: 0.8103 (mmt) REVERT: B 369 GLU cc_start: 0.8281 (tp30) cc_final: 0.8080 (tp30) REVERT: B 637 MET cc_start: 0.7851 (ttm) cc_final: 0.7449 (ttm) REVERT: C 426 MET cc_start: 0.8199 (ttm) cc_final: 0.7962 (ttp) REVERT: C 637 MET cc_start: 0.7622 (ttm) cc_final: 0.7401 (ttm) REVERT: C 987 MET cc_start: 0.8802 (mmt) cc_final: 0.8221 (mmm) REVERT: E 277 MET cc_start: 0.8484 (mmt) cc_final: 0.8238 (mmt) REVERT: E 637 MET cc_start: 0.7983 (ttm) cc_final: 0.7434 (ttm) REVERT: F 426 MET cc_start: 0.8247 (ttm) cc_final: 0.8017 (ttp) REVERT: F 592 LEU cc_start: 0.8034 (tt) cc_final: 0.7599 (tt) REVERT: F 987 MET cc_start: 0.8799 (mmt) cc_final: 0.8212 (mmm) outliers start: 4 outliers final: 0 residues processed: 358 average time/residue: 0.2487 time to fit residues: 141.0917 Evaluate side-chains 201 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN B 220 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D1002 ASN ** E 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 956 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.080853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057170 restraints weight = 145989.919| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 4.57 r_work: 0.3020 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39102 Z= 0.162 Angle : 0.611 8.857 52782 Z= 0.308 Chirality : 0.040 0.219 6000 Planarity : 0.005 0.071 6570 Dihedral : 7.807 145.326 5244 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.31 % Favored : 96.56 % Rotamer: Outliers : 0.51 % Allowed : 6.32 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4686 helix: 1.03 (0.10), residues: 2430 sheet: -1.15 (0.21), residues: 678 loop : 0.19 (0.17), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 252 TYR 0.030 0.002 TYR F 591 PHE 0.019 0.002 PHE C 581 TRP 0.013 0.001 TRP C 322 HIS 0.004 0.001 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00358 (39102) covalent geometry : angle 0.61079 (52782) hydrogen bonds : bond 0.04546 ( 1745) hydrogen bonds : angle 5.05730 ( 5166) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.9136 (mtt) cc_final: 0.8857 (mmm) REVERT: A 299 PHE cc_start: 0.8949 (m-80) cc_final: 0.8724 (m-80) REVERT: A 426 MET cc_start: 0.9201 (ttm) cc_final: 0.8909 (ptm) REVERT: B 239 MET cc_start: 0.8918 (mtm) cc_final: 0.8655 (tmm) REVERT: B 240 MET cc_start: 0.8925 (mmm) cc_final: 0.8651 (mmm) REVERT: B 277 MET cc_start: 0.8730 (mmt) cc_final: 0.8227 (mmt) REVERT: B 369 GLU cc_start: 0.9006 (tp30) cc_final: 0.8563 (tp30) REVERT: C 637 MET cc_start: 0.8445 (ttm) cc_final: 0.8136 (ttm) REVERT: D 277 MET cc_start: 0.9150 (mtt) cc_final: 0.8649 (tpp) REVERT: D 299 PHE cc_start: 0.8985 (m-80) cc_final: 0.8757 (m-80) REVERT: D 426 MET cc_start: 0.9194 (ttm) cc_final: 0.8904 (ptm) REVERT: E 239 MET cc_start: 0.8941 (mtm) cc_final: 0.8652 (tmm) REVERT: E 240 MET cc_start: 0.8968 (mmm) cc_final: 0.8730 (mmm) REVERT: E 277 MET cc_start: 0.8854 (mmt) cc_final: 0.8358 (mmt) REVERT: E 637 MET cc_start: 0.8557 (ttm) cc_final: 0.8308 (ttm) REVERT: F 277 MET cc_start: 0.9007 (ttm) cc_final: 0.8801 (mmm) outliers start: 22 outliers final: 14 residues processed: 247 average time/residue: 0.2304 time to fit residues: 95.2664 Evaluate side-chains 215 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain F residue 956 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 402 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 467 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 449 optimal weight: 3.9990 chunk 420 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 338 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN C 956 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN F 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.080411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056877 restraints weight = 145408.073| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.49 r_work: 0.3018 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39102 Z= 0.151 Angle : 0.575 8.965 52782 Z= 0.288 Chirality : 0.039 0.190 6000 Planarity : 0.004 0.070 6570 Dihedral : 7.295 149.826 5244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 0.62 % Allowed : 8.15 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.13), residues: 4686 helix: 1.15 (0.10), residues: 2454 sheet: -1.26 (0.21), residues: 690 loop : 0.22 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 252 TYR 0.017 0.001 TYR C 591 PHE 0.016 0.001 PHE C 581 TRP 0.011 0.001 TRP F 322 HIS 0.003 0.001 HIS C 492 Details of bonding type rmsd covalent geometry : bond 0.00338 (39102) covalent geometry : angle 0.57478 (52782) hydrogen bonds : bond 0.03941 ( 1745) hydrogen bonds : angle 4.83816 ( 5166) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.9253 (mpp) cc_final: 0.9017 (mpp) REVERT: A 299 PHE cc_start: 0.8983 (m-80) cc_final: 0.8731 (m-80) REVERT: A 426 MET cc_start: 0.9231 (ttm) cc_final: 0.8991 (ptm) REVERT: A 1003 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9045 (mt) REVERT: B 239 MET cc_start: 0.8953 (mtm) cc_final: 0.8662 (tmm) REVERT: B 240 MET cc_start: 0.8965 (mmm) cc_final: 0.8695 (mmm) REVERT: B 277 MET cc_start: 0.8730 (mmt) cc_final: 0.8364 (mmt) REVERT: B 369 GLU cc_start: 0.8927 (tp30) cc_final: 0.8480 (tp30) REVERT: B 1019 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8997 (mp0) REVERT: C 527 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 587 GLU cc_start: 0.9087 (mp0) cc_final: 0.8838 (pm20) REVERT: C 637 MET cc_start: 0.8549 (ttm) cc_final: 0.8163 (ttm) REVERT: C 987 MET cc_start: 0.9160 (mmt) cc_final: 0.8694 (mmm) REVERT: D 205 MET cc_start: 0.9261 (mpp) cc_final: 0.9012 (mpp) REVERT: D 277 MET cc_start: 0.9086 (mtt) cc_final: 0.8811 (mmm) REVERT: D 299 PHE cc_start: 0.8954 (m-80) cc_final: 0.8702 (m-80) REVERT: D 426 MET cc_start: 0.9228 (ttm) cc_final: 0.8992 (ptm) REVERT: D 1003 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9055 (mt) REVERT: E 239 MET cc_start: 0.8968 (mtm) cc_final: 0.8664 (tmm) REVERT: E 240 MET cc_start: 0.8974 (mmm) cc_final: 0.8708 (mmm) REVERT: E 277 MET cc_start: 0.8915 (mmt) cc_final: 0.8487 (mmt) REVERT: E 637 MET cc_start: 0.8426 (ttm) cc_final: 0.8193 (ttm) REVERT: E 1019 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8916 (mp0) REVERT: F 277 MET cc_start: 0.8981 (ttm) cc_final: 0.8780 (mmm) REVERT: F 632 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: F 987 MET cc_start: 0.9155 (mmt) cc_final: 0.8686 (mmm) outliers start: 27 outliers final: 16 residues processed: 253 average time/residue: 0.2263 time to fit residues: 95.4159 Evaluate side-chains 234 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 313 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 341 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.080302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056690 restraints weight = 144901.984| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.58 r_work: 0.3008 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39102 Z= 0.141 Angle : 0.564 9.683 52782 Z= 0.280 Chirality : 0.038 0.190 6000 Planarity : 0.004 0.070 6570 Dihedral : 7.100 150.782 5244 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % Rotamer: Outliers : 1.11 % Allowed : 9.61 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.13), residues: 4686 helix: 1.29 (0.10), residues: 2454 sheet: -1.20 (0.21), residues: 672 loop : 0.13 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 588 TYR 0.041 0.001 TYR B 591 PHE 0.015 0.001 PHE E 650 TRP 0.010 0.001 TRP C 322 HIS 0.003 0.001 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00315 (39102) covalent geometry : angle 0.56434 (52782) hydrogen bonds : bond 0.03650 ( 1745) hydrogen bonds : angle 4.69167 ( 5166) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.8786 (ttm) cc_final: 0.8438 (mmt) REVERT: A 299 PHE cc_start: 0.9008 (m-80) cc_final: 0.8750 (m-80) REVERT: A 572 TYR cc_start: 0.8645 (t80) cc_final: 0.8411 (t80) REVERT: A 1003 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9060 (mt) REVERT: B 239 MET cc_start: 0.8969 (mtm) cc_final: 0.8668 (tmm) REVERT: B 240 MET cc_start: 0.9010 (mmm) cc_final: 0.8780 (mmm) REVERT: B 277 MET cc_start: 0.8792 (mmt) cc_final: 0.8288 (mmt) REVERT: B 369 GLU cc_start: 0.8921 (tp30) cc_final: 0.8373 (tp30) REVERT: B 1019 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: C 277 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (mmt) REVERT: C 591 TYR cc_start: 0.8303 (m-80) cc_final: 0.8089 (m-80) REVERT: C 637 MET cc_start: 0.8544 (ttm) cc_final: 0.8258 (ttm) REVERT: C 987 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8683 (mmm) REVERT: C 1019 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: D 299 PHE cc_start: 0.8970 (m-80) cc_final: 0.8710 (m-80) REVERT: D 572 TYR cc_start: 0.8638 (t80) cc_final: 0.8403 (t80) REVERT: E 239 MET cc_start: 0.8970 (mtm) cc_final: 0.8665 (tmm) REVERT: E 240 MET cc_start: 0.9046 (mmm) cc_final: 0.8802 (mmm) REVERT: E 277 MET cc_start: 0.8810 (mmt) cc_final: 0.8415 (mmt) REVERT: E 637 MET cc_start: 0.8555 (ttm) cc_final: 0.8349 (ttm) REVERT: E 875 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9274 (mt) REVERT: E 1019 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8933 (mp0) REVERT: F 591 TYR cc_start: 0.8450 (m-80) cc_final: 0.8127 (m-80) REVERT: F 632 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: F 904 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9538 (mp) REVERT: F 987 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8694 (mmm) REVERT: F 1019 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8690 (mp0) outliers start: 48 outliers final: 25 residues processed: 272 average time/residue: 0.2161 time to fit residues: 98.9699 Evaluate side-chains 256 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 875 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 904 LEU Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 320 optimal weight: 30.0000 chunk 163 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 446 optimal weight: 0.8980 chunk 318 optimal weight: 7.9990 chunk 279 optimal weight: 0.0570 chunk 11 optimal weight: 8.9990 chunk 327 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 4.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 ASN E 220 HIS ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.079173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055627 restraints weight = 145685.038| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.46 r_work: 0.2978 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39102 Z= 0.180 Angle : 0.591 9.741 52782 Z= 0.292 Chirality : 0.039 0.200 6000 Planarity : 0.004 0.071 6570 Dihedral : 7.090 154.474 5244 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.34 % Allowed : 10.49 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.13), residues: 4686 helix: 1.37 (0.10), residues: 2478 sheet: -1.33 (0.21), residues: 654 loop : 0.03 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 378 TYR 0.041 0.001 TYR E 591 PHE 0.018 0.002 PHE D 575 TRP 0.008 0.001 TRP C 959 HIS 0.004 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00404 (39102) covalent geometry : angle 0.59071 (52782) hydrogen bonds : bond 0.03772 ( 1745) hydrogen bonds : angle 4.76811 ( 5166) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.8782 (ttm) cc_final: 0.8387 (mmt) REVERT: A 299 PHE cc_start: 0.9002 (m-80) cc_final: 0.8730 (m-80) REVERT: B 239 MET cc_start: 0.8989 (mtm) cc_final: 0.8678 (tmm) REVERT: B 277 MET cc_start: 0.8796 (mmt) cc_final: 0.8297 (mmt) REVERT: B 369 GLU cc_start: 0.8934 (tp30) cc_final: 0.8364 (tp30) REVERT: B 572 TYR cc_start: 0.8490 (t80) cc_final: 0.8277 (t80) REVERT: B 1019 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8999 (mp0) REVERT: C 239 MET cc_start: 0.9094 (mtm) cc_final: 0.8591 (tmm) REVERT: C 277 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8472 (mmm) REVERT: C 307 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2551 (pp) REVERT: C 591 TYR cc_start: 0.8320 (m-80) cc_final: 0.8089 (m-80) REVERT: C 637 MET cc_start: 0.8658 (ttm) cc_final: 0.8269 (ttm) REVERT: C 987 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8752 (mmm) REVERT: D 277 MET cc_start: 0.8713 (ttm) cc_final: 0.8483 (mmt) REVERT: D 299 PHE cc_start: 0.8952 (m-80) cc_final: 0.8709 (m-80) REVERT: E 239 MET cc_start: 0.9002 (mtm) cc_final: 0.8685 (tmm) REVERT: E 240 MET cc_start: 0.9085 (mmm) cc_final: 0.8812 (mmt) REVERT: E 277 MET cc_start: 0.8801 (mmt) cc_final: 0.8393 (mmt) REVERT: E 637 MET cc_start: 0.8731 (ttm) cc_final: 0.8527 (ttm) REVERT: E 1019 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.9001 (mp0) REVERT: F 239 MET cc_start: 0.8999 (mtm) cc_final: 0.8774 (tmm) REVERT: F 588 ARG cc_start: 0.7509 (ptm-80) cc_final: 0.7028 (ptm-80) REVERT: F 591 TYR cc_start: 0.8427 (m-80) cc_final: 0.7986 (m-80) REVERT: F 632 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: F 987 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8720 (mmm) outliers start: 58 outliers final: 32 residues processed: 269 average time/residue: 0.2239 time to fit residues: 101.4516 Evaluate side-chains 254 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 74 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 409 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 444 optimal weight: 4.9990 chunk 251 optimal weight: 0.0870 chunk 120 optimal weight: 10.0000 chunk 387 optimal weight: 3.9990 overall best weight: 3.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 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 = 0.3780 r_free = 0.3780 target = 0.079509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056092 restraints weight = 144703.583| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 4.45 r_work: 0.3003 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39102 Z= 0.139 Angle : 0.574 11.251 52782 Z= 0.282 Chirality : 0.039 0.217 6000 Planarity : 0.004 0.069 6570 Dihedral : 6.973 154.471 5244 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.39 % Allowed : 10.90 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.13), residues: 4686 helix: 1.46 (0.10), residues: 2466 sheet: -1.20 (0.21), residues: 672 loop : -0.06 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 588 TYR 0.013 0.001 TYR A1009 PHE 0.019 0.001 PHE A 650 TRP 0.009 0.001 TRP C 959 HIS 0.003 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00311 (39102) covalent geometry : angle 0.57383 (52782) hydrogen bonds : bond 0.03541 ( 1745) hydrogen bonds : angle 4.65379 ( 5166) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 226 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.8800 (ttm) cc_final: 0.8465 (mmt) REVERT: A 299 PHE cc_start: 0.9010 (m-80) cc_final: 0.8725 (m-80) REVERT: A 1019 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8922 (mp0) REVERT: B 239 MET cc_start: 0.8987 (mtm) cc_final: 0.8682 (tmm) REVERT: B 240 MET cc_start: 0.9104 (mmm) cc_final: 0.8832 (mmt) REVERT: B 277 MET cc_start: 0.8852 (mmt) cc_final: 0.8373 (mmt) REVERT: B 369 GLU cc_start: 0.8897 (tp30) cc_final: 0.8343 (tp30) REVERT: B 572 TYR cc_start: 0.8644 (t80) cc_final: 0.8362 (t80) REVERT: B 1019 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8995 (mp0) REVERT: C 239 MET cc_start: 0.9112 (mtm) cc_final: 0.8628 (tmm) REVERT: C 277 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8487 (mmm) REVERT: C 591 TYR cc_start: 0.8279 (m-80) cc_final: 0.8016 (m-80) REVERT: C 637 MET cc_start: 0.8589 (ttm) cc_final: 0.8295 (ttm) REVERT: C 987 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8709 (mmm) REVERT: D 277 MET cc_start: 0.8710 (ttm) cc_final: 0.8453 (mmt) REVERT: D 299 PHE cc_start: 0.9003 (m-80) cc_final: 0.8713 (m-80) REVERT: D 1019 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8916 (mp0) REVERT: E 277 MET cc_start: 0.8823 (mmt) cc_final: 0.8429 (mmt) REVERT: E 637 MET cc_start: 0.8596 (ttm) cc_final: 0.8390 (ttm) REVERT: F 239 MET cc_start: 0.9004 (mtm) cc_final: 0.8795 (tmm) REVERT: F 277 MET cc_start: 0.8882 (mmm) cc_final: 0.8673 (mmt) REVERT: F 405 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8735 (mm) REVERT: F 588 ARG cc_start: 0.7480 (ptm-80) cc_final: 0.6952 (ptm-80) REVERT: F 591 TYR cc_start: 0.8188 (m-80) cc_final: 0.7765 (m-80) REVERT: F 632 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8469 (m-80) REVERT: F 987 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8863 (mmm) outliers start: 60 outliers final: 36 residues processed: 263 average time/residue: 0.2235 time to fit residues: 98.7162 Evaluate side-chains 259 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 292 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 442 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 354 optimal weight: 0.7980 chunk 326 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 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 = 0.3783 r_free = 0.3783 target = 0.079678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056260 restraints weight = 145170.111| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.48 r_work: 0.3008 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39102 Z= 0.130 Angle : 0.570 11.743 52782 Z= 0.278 Chirality : 0.038 0.204 6000 Planarity : 0.004 0.069 6570 Dihedral : 6.865 153.388 5244 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.18 % Allowed : 11.78 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.13), residues: 4686 helix: 1.53 (0.10), residues: 2466 sheet: -1.15 (0.21), residues: 672 loop : -0.05 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 588 TYR 0.012 0.001 TYR A1009 PHE 0.017 0.001 PHE A 650 TRP 0.009 0.001 TRP F 959 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00291 (39102) covalent geometry : angle 0.56999 (52782) hydrogen bonds : bond 0.03407 ( 1745) hydrogen bonds : angle 4.59737 ( 5166) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.8974 (m-80) cc_final: 0.8685 (m-80) REVERT: B 239 MET cc_start: 0.8990 (mtm) cc_final: 0.8681 (tmm) REVERT: B 240 MET cc_start: 0.9092 (mmm) cc_final: 0.8847 (mmt) REVERT: B 277 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8391 (mmt) REVERT: B 369 GLU cc_start: 0.8863 (tp30) cc_final: 0.8450 (tp30) REVERT: B 572 TYR cc_start: 0.8601 (t80) cc_final: 0.8401 (t80) REVERT: B 591 TYR cc_start: 0.8545 (m-80) cc_final: 0.8328 (m-80) REVERT: B 1019 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8995 (mp0) REVERT: C 239 MET cc_start: 0.9093 (mtm) cc_final: 0.8603 (tmm) REVERT: C 277 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8460 (mmm) REVERT: C 405 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8742 (mm) REVERT: C 591 TYR cc_start: 0.8260 (m-80) cc_final: 0.7986 (m-80) REVERT: C 987 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8862 (mmm) REVERT: D 277 MET cc_start: 0.8741 (ttm) cc_final: 0.8444 (mmt) REVERT: D 299 PHE cc_start: 0.8971 (m-80) cc_final: 0.8690 (m-80) REVERT: E 239 MET cc_start: 0.9008 (mtm) cc_final: 0.8724 (tmm) REVERT: E 277 MET cc_start: 0.8904 (mmt) cc_final: 0.8482 (mmt) REVERT: F 239 MET cc_start: 0.9012 (mtm) cc_final: 0.8799 (tmm) REVERT: F 277 MET cc_start: 0.8919 (mmm) cc_final: 0.8681 (mmt) REVERT: F 588 ARG cc_start: 0.7500 (ptm-80) cc_final: 0.6921 (ptm-80) REVERT: F 591 TYR cc_start: 0.8170 (m-80) cc_final: 0.7802 (m-80) REVERT: F 632 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: F 987 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8868 (mmm) outliers start: 51 outliers final: 37 residues processed: 255 average time/residue: 0.2219 time to fit residues: 95.0738 Evaluate side-chains 256 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 32 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 chunk 346 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 414 optimal weight: 20.0000 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 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 = 0.3778 r_free = 0.3778 target = 0.079370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.055908 restraints weight = 144862.511| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.54 r_work: 0.2987 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39102 Z= 0.142 Angle : 0.577 12.003 52782 Z= 0.282 Chirality : 0.039 0.187 6000 Planarity : 0.004 0.070 6570 Dihedral : 6.829 153.571 5244 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.46 % Allowed : 11.85 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4686 helix: 1.50 (0.10), residues: 2490 sheet: -1.16 (0.21), residues: 672 loop : -0.10 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 588 TYR 0.015 0.001 TYR A1009 PHE 0.013 0.001 PHE E 650 TRP 0.009 0.001 TRP A 959 HIS 0.003 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00320 (39102) covalent geometry : angle 0.57707 (52782) hydrogen bonds : bond 0.03454 ( 1745) hydrogen bonds : angle 4.60951 ( 5166) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 227 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.9029 (mmm) cc_final: 0.8786 (mmt) REVERT: A 284 ASN cc_start: 0.9370 (p0) cc_final: 0.9141 (t0) REVERT: A 299 PHE cc_start: 0.8956 (m-80) cc_final: 0.8665 (m-80) REVERT: B 239 MET cc_start: 0.9006 (mtm) cc_final: 0.8688 (tmm) REVERT: B 240 MET cc_start: 0.9092 (mmm) cc_final: 0.8848 (mmt) REVERT: B 277 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8391 (mmt) REVERT: B 369 GLU cc_start: 0.8888 (tp30) cc_final: 0.8442 (tp30) REVERT: B 591 TYR cc_start: 0.8547 (m-80) cc_final: 0.8299 (m-80) REVERT: C 239 MET cc_start: 0.9098 (mtm) cc_final: 0.8605 (tmm) REVERT: C 277 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8456 (mmm) REVERT: C 405 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8741 (mm) REVERT: C 591 TYR cc_start: 0.8250 (m-80) cc_final: 0.7965 (m-80) REVERT: C 987 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8863 (mmm) REVERT: C 1003 LEU cc_start: 0.9256 (mt) cc_final: 0.9021 (mt) REVERT: D 277 MET cc_start: 0.8733 (ttm) cc_final: 0.8404 (mmt) REVERT: D 299 PHE cc_start: 0.8929 (m-80) cc_final: 0.8630 (m-80) REVERT: E 239 MET cc_start: 0.8990 (mtm) cc_final: 0.8685 (tmm) REVERT: E 277 MET cc_start: 0.8909 (mmt) cc_final: 0.8486 (mmt) REVERT: E 1003 LEU cc_start: 0.9274 (mt) cc_final: 0.9048 (mt) REVERT: F 239 MET cc_start: 0.9018 (mtm) cc_final: 0.8803 (tmm) REVERT: F 277 MET cc_start: 0.8939 (mmm) cc_final: 0.8687 (mmt) REVERT: F 405 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8738 (mm) REVERT: F 588 ARG cc_start: 0.7527 (ptm-80) cc_final: 0.6936 (ptm-80) REVERT: F 591 TYR cc_start: 0.8239 (m-80) cc_final: 0.7896 (m-80) REVERT: F 632 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: F 987 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8883 (mmm) REVERT: F 1003 LEU cc_start: 0.9261 (mt) cc_final: 0.9028 (mt) outliers start: 63 outliers final: 43 residues processed: 265 average time/residue: 0.2363 time to fit residues: 104.7997 Evaluate side-chains 268 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 69 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 chunk 285 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 200 optimal weight: 0.0570 chunk 359 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 458 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 149 optimal weight: 9.9990 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 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 = 0.3791 r_free = 0.3791 target = 0.079972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056684 restraints weight = 145657.557| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.50 r_work: 0.3019 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 39102 Z= 0.116 Angle : 0.574 12.408 52782 Z= 0.279 Chirality : 0.038 0.178 6000 Planarity : 0.004 0.068 6570 Dihedral : 6.731 151.699 5244 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.23 % Allowed : 12.15 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.13), residues: 4686 helix: 1.55 (0.10), residues: 2466 sheet: -1.11 (0.21), residues: 672 loop : -0.03 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 588 TYR 0.020 0.001 TYR B 572 PHE 0.016 0.001 PHE A 568 TRP 0.010 0.001 TRP D 959 HIS 0.003 0.001 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00259 (39102) covalent geometry : angle 0.57447 (52782) hydrogen bonds : bond 0.03274 ( 1745) hydrogen bonds : angle 4.53961 ( 5166) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.9048 (mmm) cc_final: 0.8834 (mmt) REVERT: A 284 ASN cc_start: 0.9354 (p0) cc_final: 0.9132 (t0) REVERT: A 299 PHE cc_start: 0.8928 (m-80) cc_final: 0.8632 (m-80) REVERT: B 239 MET cc_start: 0.8995 (mtm) cc_final: 0.8688 (tmm) REVERT: B 240 MET cc_start: 0.9094 (mmm) cc_final: 0.8845 (mmt) REVERT: B 277 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8407 (mmt) REVERT: B 369 GLU cc_start: 0.8873 (tp30) cc_final: 0.8453 (tp30) REVERT: B 591 TYR cc_start: 0.8489 (m-80) cc_final: 0.8237 (m-80) REVERT: C 239 MET cc_start: 0.9085 (mtm) cc_final: 0.8597 (tmm) REVERT: C 277 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8460 (mmm) REVERT: C 405 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8647 (mm) REVERT: C 591 TYR cc_start: 0.8178 (m-80) cc_final: 0.7930 (m-80) REVERT: C 987 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8846 (mmm) REVERT: D 277 MET cc_start: 0.8748 (ttm) cc_final: 0.8423 (mmt) REVERT: D 299 PHE cc_start: 0.8934 (m-80) cc_final: 0.8646 (m-80) REVERT: E 239 MET cc_start: 0.8983 (mtm) cc_final: 0.8692 (tmm) REVERT: E 277 MET cc_start: 0.8934 (mmt) cc_final: 0.8517 (mmt) REVERT: E 572 TYR cc_start: 0.8441 (t80) cc_final: 0.8219 (t80) REVERT: F 239 MET cc_start: 0.9002 (mtm) cc_final: 0.8799 (tmm) REVERT: F 405 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8639 (mm) REVERT: F 588 ARG cc_start: 0.7478 (ptm-80) cc_final: 0.6919 (ptm-80) REVERT: F 591 TYR cc_start: 0.8421 (m-80) cc_final: 0.8082 (m-80) REVERT: F 632 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8539 (m-80) REVERT: F 987 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8874 (mmm) outliers start: 53 outliers final: 43 residues processed: 258 average time/residue: 0.2287 time to fit residues: 100.1280 Evaluate side-chains 269 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 397 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 413 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 391 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 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 = 0.3769 r_free = 0.3769 target = 0.078851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055408 restraints weight = 145869.604| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.49 r_work: 0.2988 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39102 Z= 0.165 Angle : 0.602 12.593 52782 Z= 0.294 Chirality : 0.039 0.187 6000 Planarity : 0.004 0.070 6570 Dihedral : 6.667 154.121 5244 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.34 % Allowed : 12.25 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.13), residues: 4686 helix: 1.53 (0.10), residues: 2484 sheet: -1.21 (0.21), residues: 654 loop : -0.10 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 588 TYR 0.014 0.001 TYR B 572 PHE 0.013 0.001 PHE E 650 TRP 0.009 0.001 TRP D 959 HIS 0.004 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00372 (39102) covalent geometry : angle 0.60150 (52782) hydrogen bonds : bond 0.03540 ( 1745) hydrogen bonds : angle 4.65767 ( 5166) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9372 Ramachandran restraints generated. 4686 Oldfield, 0 Emsley, 4686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: 0.9018 (mmm) cc_final: 0.8785 (mmt) REVERT: A 284 ASN cc_start: 0.9389 (p0) cc_final: 0.9147 (t0) REVERT: A 299 PHE cc_start: 0.8918 (m-80) cc_final: 0.8608 (m-80) REVERT: A 426 MET cc_start: 0.9305 (ttm) cc_final: 0.8937 (ptm) REVERT: B 239 MET cc_start: 0.9006 (mtm) cc_final: 0.8683 (tmm) REVERT: B 240 MET cc_start: 0.9101 (mmm) cc_final: 0.8854 (mmt) REVERT: B 277 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8303 (mmt) REVERT: B 369 GLU cc_start: 0.8905 (tp30) cc_final: 0.8565 (tp30) REVERT: B 591 TYR cc_start: 0.8578 (m-80) cc_final: 0.8276 (m-80) REVERT: B 981 LEU cc_start: 0.9066 (mt) cc_final: 0.8839 (mt) REVERT: C 239 MET cc_start: 0.9089 (mtm) cc_final: 0.8594 (tmm) REVERT: C 277 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: C 405 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8737 (mm) REVERT: C 591 TYR cc_start: 0.8338 (m-80) cc_final: 0.8102 (m-80) REVERT: C 987 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8888 (mmm) REVERT: D 299 PHE cc_start: 0.8935 (m-80) cc_final: 0.8638 (m-80) REVERT: D 426 MET cc_start: 0.9300 (ttm) cc_final: 0.8936 (ptm) REVERT: E 239 MET cc_start: 0.9001 (mtm) cc_final: 0.8687 (tmm) REVERT: E 277 MET cc_start: 0.8916 (mmt) cc_final: 0.8482 (mmt) REVERT: E 981 LEU cc_start: 0.9071 (mt) cc_final: 0.8839 (mt) REVERT: F 239 MET cc_start: 0.9011 (mtm) cc_final: 0.8802 (tmm) REVERT: F 277 MET cc_start: 0.8762 (mmm) cc_final: 0.8513 (mmt) REVERT: F 405 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8699 (mm) REVERT: F 588 ARG cc_start: 0.7612 (ptm-80) cc_final: 0.7227 (ptm-80) REVERT: F 591 TYR cc_start: 0.8413 (m-80) cc_final: 0.8052 (m-80) REVERT: F 632 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: F 987 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8911 (mmm) outliers start: 58 outliers final: 49 residues processed: 260 average time/residue: 0.2396 time to fit residues: 104.2086 Evaluate side-chains 280 residues out of total 4326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 764 THR Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 505 MET Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 987 MET Chi-restraints excluded: chain C residue 1019 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 527 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 987 MET Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 345 optimal weight: 30.0000 chunk 358 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.0170 chunk 125 optimal weight: 0.9990 chunk 65 optimal weight: 0.0370 chunk 330 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 674 HIS ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057625 restraints weight = 145396.191| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.51 r_work: 0.3046 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39102 Z= 0.100 Angle : 0.578 12.981 52782 Z= 0.278 Chirality : 0.038 0.179 6000 Planarity : 0.004 0.066 6570 Dihedral : 6.411 148.336 5244 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.09 % Allowed : 12.52 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 4686 helix: 1.59 (0.11), residues: 2472 sheet: -1.05 (0.21), residues: 672 loop : -0.02 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 588 TYR 0.017 0.001 TYR E 572 PHE 0.014 0.001 PHE A 568 TRP 0.010 0.001 TRP D 959 HIS 0.003 0.000 HIS F 492 Details of bonding type rmsd covalent geometry : bond 0.00216 (39102) covalent geometry : angle 0.57850 (52782) hydrogen bonds : bond 0.03074 ( 1745) hydrogen bonds : angle 4.46660 ( 5166) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9305.17 seconds wall clock time: 160 minutes 58.24 seconds (9658.24 seconds total)