Starting phenix.real_space_refine on Fri Feb 23 12:54:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_32119_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_32119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_32119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_32119_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vtp_32119/02_2024/7vtp_32119_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 949": "OD1" <-> "OD2" Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 563": "OE1" <-> "OE2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B GLU 640": "OE1" <-> "OE2" Residue "B ASP 641": "OD1" <-> "OD2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 563": "OE1" <-> "OE2" Residue "C PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 613": "OE1" <-> "OE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 949": "OD1" <-> "OD2" Residue "C PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 403": "OE1" <-> "OE2" Residue "D TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 949": "OD1" <-> "OD2" Residue "D TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 305": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 389": "OE1" <-> "OE2" Residue "E PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 403": "OE1" <-> "OE2" Residue "E PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 613": "OE1" <-> "OE2" Residue "E GLU 640": "OE1" <-> "OE2" Residue "E ASP 641": "OD1" <-> "OD2" Residue "E TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "F GLU 486": "OE1" <-> "OE2" Residue "F TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 563": "OE1" <-> "OE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 613": "OE1" <-> "OE2" Residue "F TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 949": "OD1" <-> "OD2" Residue "F TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 19.56, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 15.43 Conformation dependent library (CDL) restraints added in 7.3 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... running ksdssp... Secondary structure from input PDB file: 210 helices and 22 sheets defined 47.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.66 Creating SS restraints... Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.717A pdb=" N LYS A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.518A pdb=" N LEU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.380A pdb=" N PHE A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 486 through 492 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 558 through 563 Processing helix chain 'A' and resid 569 through 583 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 603 through 617 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.920A pdb=" N ASP A 648 " --> pdb=" O GLN A 644 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 672 Processing helix chain 'A' and resid 727 through 739 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 754 through 765 Processing helix chain 'A' and resid 784 through 796 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 811 through 822 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 851 removed outlier: 3.711A pdb=" N LEU A 847 " --> pdb=" O CYS A 844 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 848 " --> pdb=" O GLN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 removed outlier: 3.778A pdb=" N LYS A 878 " --> pdb=" O ILE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 910 removed outlier: 4.673A pdb=" N ALA A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 removed outlier: 3.699A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 removed outlier: 4.085A pdb=" N TRP A 959 " --> pdb=" O HIS A 956 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 961 " --> pdb=" O CYS A 958 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 966 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1012 through 1024 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.718A pdb=" N LYS B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 352 through 361 Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.441A pdb=" N PHE B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 439 through 450 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 486 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 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 558 through 563 Processing helix chain 'B' and resid 569 through 583 Processing helix chain 'B' and resid 588 through 596 Processing helix chain 'B' and resid 603 through 617 Processing helix chain 'B' and resid 628 through 637 Processing helix chain 'B' and resid 640 through 649 removed outlier: 3.817A pdb=" N ASP B 648 " --> pdb=" O GLN B 644 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 672 Processing helix chain 'B' and resid 727 through 739 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 754 through 765 Processing helix chain 'B' and resid 784 through 796 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 811 through 822 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 842 through 851 removed outlier: 3.559A pdb=" N GLN B 845 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 847 " --> pdb=" O CYS B 844 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA B 848 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 879 removed outlier: 3.702A pdb=" N LYS B 878 " --> pdb=" O ILE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 910 removed outlier: 4.671A pdb=" N ALA B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 936 removed outlier: 3.710A pdb=" N GLY B 935 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 967 removed outlier: 4.129A pdb=" N TRP B 959 " --> pdb=" O HIS B 956 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 961 " --> pdb=" O CYS B 958 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 966 " --> pdb=" O THR B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 993 Processing helix chain 'B' and resid 1012 through 1024 Processing helix chain 'C' and resid 136 through 147 Processing helix chain 'C' and resid 164 through 167 No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.693A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) Proline residue: C 294 - end of helix Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 389 through 400 Processing helix chain 'C' and resid 403 through 410 removed outlier: 4.379A pdb=" N PHE C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'C' and resid 463 through 479 Processing helix chain 'C' and resid 486 through 492 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 569 through 583 Processing helix chain 'C' and resid 588 through 596 Processing helix chain 'C' and resid 603 through 617 Processing helix chain 'C' and resid 628 through 637 Processing helix chain 'C' and resid 640 through 649 removed outlier: 3.799A pdb=" N ASP C 648 " --> pdb=" O GLN C 644 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 727 through 739 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 754 through 765 Processing helix chain 'C' and resid 784 through 796 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 811 through 822 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 851 removed outlier: 3.747A pdb=" N LEU C 847 " --> pdb=" O CYS C 844 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 848 " --> pdb=" O GLN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 879 removed outlier: 3.711A pdb=" N LYS C 878 " --> pdb=" O ILE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 910 Processing helix chain 'C' and resid 925 through 936 removed outlier: 3.691A pdb=" N GLY C 935 " --> pdb=" O LEU C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 967 removed outlier: 3.984A pdb=" N TRP C 959 " --> pdb=" O HIS C 956 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 961 " --> pdb=" O CYS C 958 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 966 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 993 Processing helix chain 'C' and resid 1012 through 1024 Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 164 through 167 No H-bonds generated for 'chain 'D' and resid 164 through 167' Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 287 through 296 removed outlier: 3.718A pdb=" N LYS D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) Proline residue: D 294 - end of helix Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.517A pdb=" N LEU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 389 through 400 Processing helix chain 'D' and resid 403 through 410 removed outlier: 4.381A pdb=" N PHE D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 439 through 450 Processing helix chain 'D' and resid 463 through 479 Processing helix chain 'D' and resid 486 through 492 Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 569 through 583 Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 603 through 617 Processing helix chain 'D' and resid 628 through 637 Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.920A pdb=" N ASP D 648 " --> pdb=" O GLN D 644 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 672 Processing helix chain 'D' and resid 727 through 739 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 754 through 765 Processing helix chain 'D' and resid 784 through 796 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 811 through 822 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 851 removed outlier: 3.711A pdb=" N LEU D 847 " --> pdb=" O CYS D 844 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 848 " --> pdb=" O GLN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 879 removed outlier: 3.778A pdb=" N LYS D 878 " --> pdb=" O ILE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 910 removed outlier: 4.673A pdb=" N ALA D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 936 removed outlier: 3.699A pdb=" N GLY D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 967 removed outlier: 4.085A pdb=" N TRP D 959 " --> pdb=" O HIS D 956 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 961 " --> pdb=" O CYS D 958 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 966 " --> pdb=" O THR D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 993 Processing helix chain 'D' and resid 1012 through 1024 Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 164 through 167 No H-bonds generated for 'chain 'E' and resid 164 through 167' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.721A pdb=" N LYS E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) Proline residue: E 294 - end of helix Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 352 through 361 Processing helix chain 'E' and resid 375 through 385 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 403 through 410 removed outlier: 4.441A pdb=" N PHE E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 439 through 450 Processing helix chain 'E' and resid 463 through 479 Processing helix chain 'E' and resid 486 through 491 Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 558 through 563 Processing helix chain 'E' and resid 569 through 583 Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'E' and resid 603 through 617 Processing helix chain 'E' and resid 628 through 637 Processing helix chain 'E' and resid 640 through 649 removed outlier: 3.749A pdb=" N ASP E 648 " --> pdb=" O GLN E 644 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 660 through 672 Processing helix chain 'E' and resid 727 through 739 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 754 through 765 Processing helix chain 'E' and resid 784 through 796 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 811 through 822 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 842 through 851 removed outlier: 3.558A pdb=" N GLN E 845 " --> pdb=" O ALA E 842 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 847 " --> pdb=" O CYS E 844 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA E 848 " --> pdb=" O GLN E 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 868 through 879 removed outlier: 3.703A pdb=" N LYS E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 899 through 910 removed outlier: 4.673A pdb=" N ALA E 903 " --> pdb=" O VAL E 899 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 936 removed outlier: 3.712A pdb=" N GLY E 935 " --> pdb=" O LEU E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 955 through 967 removed outlier: 4.127A pdb=" N TRP E 959 " --> pdb=" O HIS E 956 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 961 " --> pdb=" O CYS E 958 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 966 " --> pdb=" O THR E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 993 Processing helix chain 'E' and resid 1012 through 1024 Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 164 through 167 No H-bonds generated for 'chain 'F' and resid 164 through 167' Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 287 through 296 removed outlier: 3.685A pdb=" N LYS F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) Proline residue: F 294 - end of helix Processing helix chain 'F' and resid 328 through 336 Processing helix chain 'F' and resid 352 through 361 removed outlier: 3.582A pdb=" N LEU F 361 " --> pdb=" O LYS F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 385 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.379A pdb=" N PHE F 410 " --> pdb=" O PHE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 439 through 450 Processing helix chain 'F' and resid 463 through 479 Processing helix chain 'F' and resid 486 through 492 Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 558 through 563 Processing helix chain 'F' and resid 569 through 583 Processing helix chain 'F' and resid 588 through 596 Processing helix chain 'F' and resid 603 through 617 Processing helix chain 'F' and resid 628 through 637 Processing helix chain 'F' and resid 640 through 649 removed outlier: 3.791A pdb=" N ASP F 648 " --> pdb=" O GLN F 644 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TYR F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 672 Processing helix chain 'F' and resid 727 through 739 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 754 through 765 Processing helix chain 'F' and resid 784 through 796 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 811 through 822 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 851 removed outlier: 3.759A pdb=" N LEU F 847 " --> pdb=" O CYS F 844 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA F 848 " --> pdb=" O GLN F 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 868 through 879 removed outlier: 3.777A pdb=" N LYS F 878 " --> pdb=" O ILE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 910 Processing helix chain 'F' and resid 925 through 936 removed outlier: 3.689A pdb=" N GLY F 935 " --> pdb=" O LEU F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 955 through 967 removed outlier: 3.978A pdb=" N TRP F 959 " --> pdb=" O HIS F 956 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 961 " --> pdb=" O CYS F 958 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR F 966 " --> pdb=" O THR F 963 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 993 Processing helix chain 'F' and resid 1012 through 1024 Processing sheet with id= A, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.005A pdb=" N GLY A 372 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE A 174 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE A 370 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 346 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE A 224 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 348 " --> pdb=" O PHE A 224 " (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= B, first strand: chain 'A' and resid 653 through 657 Processing sheet with id= C, first strand: chain 'A' and resid 745 through 747 removed outlier: 6.724A pdb=" N ARG A 774 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU A 802 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS A 831 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG A 859 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS A 888 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 916 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 945 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS A 973 " --> pdb=" O LEU A 946 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN A1002 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A1029 " --> pdb=" O LEU A1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.992A pdb=" N GLY B 372 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE B 174 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE B 370 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 346 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE B 224 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 348 " --> pdb=" O PHE B 224 " (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= E, first strand: chain 'B' and resid 503 through 506 Processing sheet with id= F, first strand: chain 'B' and resid 653 through 657 Processing sheet with id= G, first strand: chain 'B' and resid 745 through 747 removed outlier: 6.627A pdb=" N ARG B 774 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU B 802 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS B 831 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG B 859 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS B 888 " --> pdb=" O LEU B 860 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS B 916 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 945 " --> pdb=" O LEU B 917 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS B 973 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN B1002 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR B1029 " --> pdb=" O LEU B1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.955A pdb=" N GLY C 372 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE C 174 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 370 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 346 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE C 224 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE C 348 " --> pdb=" O PHE C 224 " (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= I, first strand: chain 'C' and resid 503 through 506 Processing sheet with id= J, first strand: chain 'C' and resid 653 through 657 Processing sheet with id= K, first strand: chain 'C' and resid 745 through 747 removed outlier: 6.686A pdb=" N ARG C 774 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU C 802 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS C 831 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG C 859 " --> pdb=" O LEU C 832 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 888 " --> pdb=" O LEU C 860 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N HIS C 916 " --> pdb=" O LEU C 889 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL C 945 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS C 973 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN C1002 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C1029 " --> pdb=" O LEU C1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 172 through 175 removed outlier: 4.003A pdb=" N GLY D 372 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE D 174 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE D 370 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 346 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N PHE D 224 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 348 " --> pdb=" O PHE D 224 " (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= M, first strand: chain 'D' and resid 653 through 657 Processing sheet with id= N, first strand: chain 'D' and resid 745 through 747 removed outlier: 6.724A pdb=" N ARG D 774 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU D 802 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS D 831 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG D 859 " --> pdb=" O LEU D 832 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS D 888 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS D 916 " --> pdb=" O LEU D 889 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 945 " --> pdb=" O LEU D 917 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS D 973 " --> pdb=" O LEU D 946 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN D1002 " --> pdb=" O LEU D 974 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR D1029 " --> pdb=" O LEU D1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.977A pdb=" N GLY E 372 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE E 174 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE E 370 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 346 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE E 224 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE E 348 " --> pdb=" O PHE E 224 " (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= P, first strand: chain 'E' and resid 503 through 506 Processing sheet with id= Q, first strand: chain 'E' and resid 653 through 657 Processing sheet with id= R, first strand: chain 'E' and resid 745 through 747 removed outlier: 6.733A pdb=" N ARG E 774 " --> pdb=" O LEU E 746 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU E 802 " --> pdb=" O LEU E 775 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS E 831 " --> pdb=" O LEU E 803 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG E 859 " --> pdb=" O LEU E 832 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS E 888 " --> pdb=" O LEU E 860 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N HIS E 916 " --> pdb=" O LEU E 889 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 945 " --> pdb=" O LEU E 917 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS E 973 " --> pdb=" O LEU E 946 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN E1002 " --> pdb=" O LEU E 974 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR E1029 " --> pdb=" O LEU E1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.958A pdb=" N GLY F 372 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE F 174 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE F 370 " --> pdb=" O ILE F 174 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU F 346 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE F 224 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 348 " --> pdb=" O PHE F 224 " (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= T, first strand: chain 'F' and resid 503 through 506 Processing sheet with id= U, first strand: chain 'F' and resid 653 through 657 Processing sheet with id= V, first strand: chain 'F' and resid 745 through 747 removed outlier: 6.687A pdb=" N ARG F 774 " --> pdb=" O LEU F 746 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU F 802 " --> pdb=" O LEU F 775 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS F 831 " --> pdb=" O LEU F 803 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG F 859 " --> pdb=" O LEU F 832 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS F 888 " --> pdb=" O LEU F 860 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS F 916 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL F 945 " --> pdb=" O LEU F 917 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS F 973 " --> pdb=" O LEU F 946 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN F1002 " --> pdb=" O LEU F 974 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR F1029 " --> pdb=" O LEU F1003 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 1431 hydrogen bonds defined for protein. 4029 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: 14.33 Time building geometry restraints manager: 16.38 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: 93.66 - 103.05: 228 103.05 - 112.44: 20626 112.44 - 121.83: 23990 121.83 - 131.22: 7830 131.22 - 140.61: 108 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: 564 2.67 - 3.23: 37407 3.23 - 3.78: 59926 3.78 - 4.34: 82705 4.34 - 4.90: 133413 Nonbonded interactions: 314015 Sorted by model distance: nonbonded pdb=" OH TYR C 632 " pdb=" OD1 ASP C 662 " model vdw 2.111 2.440 nonbonded pdb=" OH TYR F 632 " pdb=" OD1 ASP F 662 " model vdw 2.116 2.440 nonbonded pdb=" OH TYR B 632 " pdb=" OD1 ASP B 662 " model vdw 2.135 2.440 nonbonded pdb=" OH TYR E 632 " pdb=" OD1 ASP E 662 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR A 632 " pdb=" OD1 ASP A 662 " model vdw 2.160 2.440 ... (remaining 314010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.370 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: 0.040 Extract box with map and model: 4.010 Check model and map are aligned: 0.520 Set scattering table: 0.340 Process input model: 102.020 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.900 ------------------------------------------------------------------------------- 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= 0.277 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 : 11.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.002 TRP E 322 HIS 0.004 0.001 HIS D 663 PHE 0.014 0.001 PHE B 396 TYR 0.019 0.001 TYR C1009 ARG 0.004 0.000 ARG F 605 *********************** 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 fitting. rotamer outliers: 4 poor density : 354 time to evaluate : 4.347 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: 0.8081 (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: 0.5463 time to fit residues: 307.9859 Evaluate side-chains 201 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 430 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS D 220 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN D1002 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 956 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39102 Z= 0.209 Angle : 0.566 8.464 52782 Z= 0.284 Chirality : 0.038 0.180 6000 Planarity : 0.004 0.074 6570 Dihedral : 7.890 144.999 5244 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 0.37 % Allowed : 6.60 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4686 helix: 1.02 (0.11), residues: 2436 sheet: -1.05 (0.21), residues: 660 loop : 0.16 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 322 HIS 0.003 0.001 HIS C 492 PHE 0.022 0.001 PHE C 581 TYR 0.029 0.001 TYR F 591 ARG 0.005 0.000 ARG E 920 *********************** 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 255 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 239 time to evaluate : 4.243 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: A 299 PHE cc_start: 0.8690 (m-80) cc_final: 0.8460 (m-80) REVERT: B 277 MET cc_start: 0.8510 (mmt) cc_final: 0.8097 (mmt) REVERT: B 369 GLU cc_start: 0.8311 (tp30) cc_final: 0.8006 (tp30) REVERT: B 426 MET cc_start: 0.8258 (ptm) cc_final: 0.8046 (ptm) REVERT: C 426 MET cc_start: 0.8205 (ttm) cc_final: 0.7967 (ttp) REVERT: C 987 MET cc_start: 0.8813 (mmt) cc_final: 0.8424 (mmm) REVERT: C 1019 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8845 (mp0) REVERT: D 277 MET cc_start: 0.8927 (mtt) cc_final: 0.8699 (mmm) REVERT: D 299 PHE cc_start: 0.8691 (m-80) cc_final: 0.8464 (m-80) REVERT: E 277 MET cc_start: 0.8555 (mmt) cc_final: 0.8176 (mmt) REVERT: E 426 MET cc_start: 0.8215 (ptm) cc_final: 0.8004 (ptm) REVERT: F 426 MET cc_start: 0.8213 (ttm) cc_final: 0.7978 (ttp) REVERT: F 987 MET cc_start: 0.8808 (mmt) cc_final: 0.8416 (mmm) REVERT: F 1019 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (mp0) outliers start: 16 outliers final: 10 residues processed: 246 average time/residue: 0.5025 time to fit residues: 205.7360 Evaluate side-chains 216 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 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 C residue 1019 GLU Chi-restraints excluded: chain D residue 592 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 Chi-restraints excluded: chain F residue 1019 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 431 optimal weight: 9.9990 chunk 465 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 427 optimal weight: 0.0270 chunk 147 optimal weight: 8.9990 chunk 345 optimal weight: 6.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 956 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN ** E 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 956 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1595 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= 0.274 Angle : 0.576 8.654 52782 Z= 0.287 Chirality : 0.038 0.195 6000 Planarity : 0.004 0.074 6570 Dihedral : 7.421 142.635 5244 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer: Outliers : 0.65 % Allowed : 8.17 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4686 helix: 1.15 (0.11), residues: 2466 sheet: -1.23 (0.21), residues: 678 loop : 0.05 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 959 HIS 0.011 0.001 HIS C 956 PHE 0.019 0.002 PHE A 575 TYR 0.018 0.001 TYR F 591 ARG 0.003 0.000 ARG D 588 *********************** 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 260 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 4.424 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 299 PHE cc_start: 0.8767 (m-80) cc_final: 0.8533 (m-80) REVERT: B 239 MET cc_start: 0.8065 (tmm) cc_final: 0.7709 (tmm) REVERT: B 277 MET cc_start: 0.8525 (mmt) cc_final: 0.8080 (mmt) REVERT: C 426 MET cc_start: 0.8214 (ttm) cc_final: 0.7983 (ttp) REVERT: C 987 MET cc_start: 0.8930 (mmt) cc_final: 0.8454 (mmm) REVERT: C 1019 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: D 299 PHE cc_start: 0.8780 (m-80) cc_final: 0.8548 (m-80) REVERT: E 239 MET cc_start: 0.8062 (tmm) cc_final: 0.7705 (tmm) REVERT: E 277 MET cc_start: 0.8576 (mmt) cc_final: 0.8169 (mmt) REVERT: F 426 MET cc_start: 0.8221 (ttm) cc_final: 0.7986 (ttp) REVERT: F 591 TYR cc_start: 0.7757 (m-80) cc_final: 0.7515 (m-80) REVERT: F 987 MET cc_start: 0.8927 (mmt) cc_final: 0.8448 (mmm) REVERT: F 1019 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8839 (mp0) outliers start: 28 outliers final: 18 residues processed: 245 average time/residue: 0.5070 time to fit residues: 207.8359 Evaluate side-chains 229 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 4.542 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 1019 GLU 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 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 1019 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 458 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 410 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** 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 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 622 GLN ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39102 Z= 0.276 Angle : 0.574 8.999 52782 Z= 0.287 Chirality : 0.038 0.193 6000 Planarity : 0.004 0.076 6570 Dihedral : 7.247 141.636 5244 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.23 % Allowed : 9.00 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4686 helix: 1.26 (0.11), residues: 2466 sheet: -1.33 (0.21), residues: 684 loop : 0.01 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 959 HIS 0.003 0.001 HIS A 522 PHE 0.018 0.002 PHE F 575 TYR 0.021 0.001 TYR D 572 ARG 0.002 0.000 ARG C 252 *********************** 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 283 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 4.649 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: A 277 MET cc_start: 0.8678 (mmt) cc_final: 0.8256 (mmt) REVERT: A 299 PHE cc_start: 0.8803 (m-80) cc_final: 0.8560 (m-80) REVERT: A 518 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: B 239 MET cc_start: 0.8074 (tmm) cc_final: 0.7848 (tmm) REVERT: B 277 MET cc_start: 0.8526 (mmt) cc_final: 0.8106 (mmt) REVERT: C 426 MET cc_start: 0.8207 (ttm) cc_final: 0.7974 (ttp) REVERT: C 987 MET cc_start: 0.8985 (mmt) cc_final: 0.8577 (mmm) REVERT: C 1019 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8765 (mp0) REVERT: D 299 PHE cc_start: 0.8813 (m-80) cc_final: 0.8576 (m-80) REVERT: D 518 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: E 239 MET cc_start: 0.8074 (tmm) cc_final: 0.7848 (tmm) REVERT: E 277 MET cc_start: 0.8578 (mmt) cc_final: 0.8190 (mmt) REVERT: F 426 MET cc_start: 0.8214 (ttm) cc_final: 0.7983 (ttp) REVERT: F 591 TYR cc_start: 0.7693 (m-80) cc_final: 0.7426 (m-80) REVERT: F 987 MET cc_start: 0.8982 (mmt) cc_final: 0.8572 (mmm) REVERT: F 1019 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8769 (mp0) outliers start: 53 outliers final: 35 residues processed: 264 average time/residue: 0.4814 time to fit residues: 211.8349 Evaluate side-chains 251 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 4.555 ------------------------------------------------------------------------------- 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 518 TYR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 949 ASP 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 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 637 MET 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 353 VAL Chi-restraints excluded: chain C residue 932 LEU 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 518 TYR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 949 ASP 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 588 ARG Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1003 LEU Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 932 LEU 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 381 optimal weight: 3.9990 chunk 260 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 390 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 0.5980 chunk 411 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39102 Z= 0.208 Angle : 0.543 9.021 52782 Z= 0.269 Chirality : 0.038 0.184 6000 Planarity : 0.004 0.074 6570 Dihedral : 7.061 141.172 5244 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.46 % Allowed : 9.88 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.13), residues: 4686 helix: 1.40 (0.11), residues: 2466 sheet: -1.19 (0.21), residues: 672 loop : 0.05 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 959 HIS 0.003 0.001 HIS F 663 PHE 0.014 0.001 PHE B 568 TYR 0.025 0.001 TYR B 591 ARG 0.002 0.000 ARG F 252 *********************** 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 286 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 223 time to evaluate : 4.541 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: A 299 PHE cc_start: 0.8781 (m-80) cc_final: 0.8544 (m-80) REVERT: A 518 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7732 (m-80) REVERT: B 239 MET cc_start: 0.8128 (tmm) cc_final: 0.7920 (tmm) REVERT: B 277 MET cc_start: 0.8532 (mmt) cc_final: 0.8077 (mmt) REVERT: B 572 TYR cc_start: 0.7037 (t80) cc_final: 0.6829 (t80) REVERT: C 426 MET cc_start: 0.8160 (ttm) cc_final: 0.7925 (ttp) REVERT: C 1019 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8739 (mp0) REVERT: D 299 PHE cc_start: 0.8795 (m-80) cc_final: 0.8561 (m-80) REVERT: D 518 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: E 239 MET cc_start: 0.8129 (tmm) cc_final: 0.7925 (tmm) REVERT: E 277 MET cc_start: 0.8539 (mmt) cc_final: 0.8151 (mmt) REVERT: E 505 MET cc_start: 0.6852 (tpt) cc_final: 0.6636 (tpt) REVERT: E 518 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: F 426 MET cc_start: 0.8183 (ttm) cc_final: 0.7950 (ttp) REVERT: F 591 TYR cc_start: 0.7613 (m-80) cc_final: 0.7357 (m-80) REVERT: F 1019 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8744 (mp0) outliers start: 63 outliers final: 43 residues processed: 266 average time/residue: 0.4853 time to fit residues: 214.7250 Evaluate side-chains 260 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 4.606 ------------------------------------------------------------------------------- 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 518 TYR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1014 THR 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 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1003 LEU 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 353 VAL Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 518 TYR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1014 THR 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 518 TYR 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 1014 THR Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 949 ASP Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 30.0000 chunk 412 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 458 optimal weight: 7.9990 chunk 380 optimal weight: 0.0870 chunk 212 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 overall best weight: 6.2166 ------------------------------------------------------------------------------- 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** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS ** E 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39102 Z= 0.334 Angle : 0.605 9.616 52782 Z= 0.300 Chirality : 0.039 0.202 6000 Planarity : 0.004 0.078 6570 Dihedral : 7.114 140.492 5244 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.76 % Allowed : 10.46 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4686 helix: 1.36 (0.11), residues: 2460 sheet: -1.41 (0.20), residues: 684 loop : 0.01 (0.17), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 959 HIS 0.004 0.001 HIS D 522 PHE 0.017 0.002 PHE B 575 TYR 0.021 0.001 TYR B 591 ARG 0.002 0.000 ARG B 588 *********************** 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 297 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 221 time to evaluate : 4.515 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 299 PHE cc_start: 0.8830 (m-80) cc_final: 0.8575 (m-80) REVERT: A 987 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7851 (mmm) REVERT: B 239 MET cc_start: 0.8170 (tmm) cc_final: 0.7923 (tmm) REVERT: B 277 MET cc_start: 0.8539 (mmt) cc_final: 0.8147 (mmt) REVERT: B 875 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8762 (mp) REVERT: C 405 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 426 MET cc_start: 0.8174 (ttm) cc_final: 0.7937 (ttp) REVERT: C 1019 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8708 (mp0) REVERT: D 277 MET cc_start: 0.8529 (mmt) cc_final: 0.8040 (mmt) REVERT: D 299 PHE cc_start: 0.8844 (m-80) cc_final: 0.8591 (m-80) REVERT: D 987 MET cc_start: 0.8720 (mmt) cc_final: 0.7835 (mmm) REVERT: E 239 MET cc_start: 0.8175 (tmm) cc_final: 0.7929 (tmm) REVERT: E 277 MET cc_start: 0.8549 (mmt) cc_final: 0.8215 (mmt) REVERT: E 505 MET cc_start: 0.6908 (tpt) cc_final: 0.6705 (tpt) REVERT: E 518 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: E 875 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8761 (mp) REVERT: F 277 MET cc_start: 0.8698 (mmt) cc_final: 0.8357 (mmt) REVERT: F 369 GLU cc_start: 0.7766 (tp30) cc_final: 0.7551 (tm-30) REVERT: F 405 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8813 (mm) REVERT: F 426 MET cc_start: 0.8165 (ttm) cc_final: 0.7929 (ttp) REVERT: F 1019 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8718 (mp0) outliers start: 76 outliers final: 50 residues processed: 275 average time/residue: 0.5274 time to fit residues: 243.3254 Evaluate side-chains 269 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 4.332 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1014 THR 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 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1003 LEU 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 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 592 LEU Chi-restraints excluded: chain D residue 949 ASP Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 518 TYR Chi-restraints excluded: chain E residue 588 ARG 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 1003 LEU Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 411 ILE Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 949 ASP Chi-restraints excluded: chain F residue 1019 GLU Chi-restraints excluded: chain F residue 1031 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 386 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 456 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 chunk 210 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2425 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= 0.223 Angle : 0.555 9.985 52782 Z= 0.274 Chirality : 0.038 0.241 6000 Planarity : 0.004 0.075 6570 Dihedral : 6.994 141.380 5244 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.76 % Allowed : 11.27 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 4686 helix: 1.44 (0.11), residues: 2460 sheet: -1.22 (0.21), residues: 672 loop : 0.05 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 959 HIS 0.003 0.001 HIS C 492 PHE 0.016 0.001 PHE B 528 TYR 0.019 0.001 TYR B 591 ARG 0.010 0.000 ARG A 588 *********************** 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 295 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 219 time to evaluate : 4.409 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 299 PHE cc_start: 0.8787 (m-80) cc_final: 0.8549 (m-80) REVERT: A 518 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: A 987 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8061 (mmm) REVERT: B 239 MET cc_start: 0.8161 (tmm) cc_final: 0.7960 (tmm) REVERT: B 254 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: B 277 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: B 875 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8727 (mp) REVERT: C 405 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8810 (mm) REVERT: C 426 MET cc_start: 0.8107 (ttm) cc_final: 0.7882 (ttp) REVERT: C 987 MET cc_start: 0.8992 (mmt) cc_final: 0.8675 (mmm) REVERT: C 1019 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8683 (mp0) REVERT: D 277 MET cc_start: 0.8421 (mmt) cc_final: 0.7910 (mmt) REVERT: D 299 PHE cc_start: 0.8810 (m-80) cc_final: 0.8578 (m-80) REVERT: D 369 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7516 (tm-30) REVERT: D 518 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: D 987 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8041 (mmm) REVERT: E 239 MET cc_start: 0.8160 (tmm) cc_final: 0.7959 (tmm) REVERT: E 254 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: E 277 MET cc_start: 0.8510 (mmt) cc_final: 0.8167 (mmt) REVERT: E 505 MET cc_start: 0.6867 (tpt) cc_final: 0.6661 (tpt) REVERT: E 518 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7736 (m-80) REVERT: E 875 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8730 (mp) REVERT: F 277 MET cc_start: 0.8683 (mmt) cc_final: 0.8334 (mmt) REVERT: F 405 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8813 (mm) REVERT: F 426 MET cc_start: 0.8118 (ttm) cc_final: 0.7899 (ttp) REVERT: F 632 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: F 987 MET cc_start: 0.8990 (mmt) cc_final: 0.8670 (mmm) REVERT: F 1019 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8692 (mp0) outliers start: 76 outliers final: 52 residues processed: 271 average time/residue: 0.4935 time to fit residues: 222.2807 Evaluate side-chains 273 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 4.351 ------------------------------------------------------------------------------- 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 518 TYR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 254 ASP 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 399 ILE Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1014 THR 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 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 518 TYR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 875 LEU Chi-restraints excluded: chain D residue 949 ASP Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1003 LEU Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 254 ASP Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 518 TYR Chi-restraints excluded: chain E residue 588 ARG 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 1003 LEU Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 445 PHE 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 949 ASP 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 282 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 89 optimal weight: 40.0000 chunk 88 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 359 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** B 220 HIS ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 GLN ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 39102 Z= 0.153 Angle : 0.538 10.105 52782 Z= 0.262 Chirality : 0.037 0.237 6000 Planarity : 0.004 0.073 6570 Dihedral : 6.748 139.949 5244 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.39 % Allowed : 11.97 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 4686 helix: 1.56 (0.11), residues: 2448 sheet: -1.03 (0.21), residues: 636 loop : 0.06 (0.17), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 959 HIS 0.002 0.000 HIS C 492 PHE 0.015 0.001 PHE A 568 TYR 0.018 0.001 TYR B 591 ARG 0.007 0.000 ARG B 296 *********************** 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 283 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 4.847 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: A 299 PHE cc_start: 0.8764 (m-80) cc_final: 0.8524 (m-80) REVERT: A 518 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7637 (m-10) REVERT: A 987 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8297 (mmm) REVERT: B 277 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8083 (mmt) REVERT: B 875 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8710 (mp) REVERT: C 405 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8831 (mm) REVERT: C 426 MET cc_start: 0.8059 (ttm) cc_final: 0.7838 (ttp) REVERT: C 987 MET cc_start: 0.9098 (mmt) cc_final: 0.8818 (mmm) REVERT: C 1019 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: D 299 PHE cc_start: 0.8757 (m-80) cc_final: 0.8502 (m-80) REVERT: D 518 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7620 (m-10) REVERT: D 987 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8177 (mmm) REVERT: E 277 MET cc_start: 0.8500 (mmt) cc_final: 0.8138 (mmt) REVERT: E 518 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: F 277 MET cc_start: 0.8586 (mmt) cc_final: 0.8356 (mmt) REVERT: F 405 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8830 (mm) REVERT: F 426 MET cc_start: 0.8110 (ttm) cc_final: 0.7889 (ttp) REVERT: F 632 TYR cc_start: 0.8420 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: F 987 MET cc_start: 0.9096 (mmt) cc_final: 0.8816 (mmm) REVERT: F 1019 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8727 (mp0) outliers start: 60 outliers final: 41 residues processed: 266 average time/residue: 0.5074 time to fit residues: 223.5194 Evaluate side-chains 254 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 201 time to evaluate : 4.454 ------------------------------------------------------------------------------- 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 518 TYR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 254 ASP 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 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 875 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 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 518 TYR Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 949 ASP Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1019 GLU Chi-restraints excluded: chain D residue 1031 VAL Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain E residue 518 TYR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 996 GLN Chi-restraints excluded: chain E residue 1014 THR Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 949 ASP 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 415 optimal weight: 20.0000 chunk 437 optimal weight: 9.9990 chunk 399 optimal weight: 8.9990 chunk 425 optimal weight: 0.8980 chunk 256 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 384 optimal weight: 0.0010 chunk 402 optimal weight: 9.9990 chunk 424 optimal weight: 9.9990 overall best weight: 4.5792 ------------------------------------------------------------------------------- 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** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 996 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 39102 Z= 0.265 Angle : 0.583 10.498 52782 Z= 0.286 Chirality : 0.038 0.187 6000 Planarity : 0.004 0.075 6570 Dihedral : 6.775 138.788 5244 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.39 % Allowed : 12.41 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4686 helix: 1.50 (0.11), residues: 2454 sheet: -1.05 (0.21), residues: 660 loop : 0.05 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 959 HIS 0.004 0.001 HIS D 220 PHE 0.016 0.001 PHE A 304 TYR 0.023 0.001 TYR B 591 ARG 0.008 0.000 ARG D 252 *********************** 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 275 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 4.569 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: A 299 PHE cc_start: 0.8786 (m-80) cc_final: 0.8518 (m-80) REVERT: A 987 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: B 277 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: B 875 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8750 (mp) REVERT: C 405 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8824 (mm) REVERT: C 426 MET cc_start: 0.8094 (ttm) cc_final: 0.7868 (ttp) REVERT: C 987 MET cc_start: 0.9027 (mmt) cc_final: 0.8691 (mmm) REVERT: C 1019 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8707 (mp0) REVERT: D 299 PHE cc_start: 0.8806 (m-80) cc_final: 0.8543 (m-80) REVERT: D 987 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8014 (mmm) REVERT: E 277 MET cc_start: 0.8504 (mmt) cc_final: 0.8184 (mmt) REVERT: F 277 MET cc_start: 0.8609 (mmt) cc_final: 0.8351 (mmt) REVERT: F 369 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7110 (tm-30) REVERT: F 405 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8827 (mm) REVERT: F 426 MET cc_start: 0.8103 (ttm) cc_final: 0.7882 (ttp) REVERT: F 632 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: F 987 MET cc_start: 0.9027 (mmt) cc_final: 0.8690 (mmm) REVERT: F 1019 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8715 (mp0) outliers start: 60 outliers final: 45 residues processed: 255 average time/residue: 0.5853 time to fit residues: 252.2876 Evaluate side-chains 263 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 4.379 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 254 ASP 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 875 LEU Chi-restraints excluded: chain B residue 996 GLN Chi-restraints excluded: chain B residue 1003 LEU Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 592 LEU Chi-restraints excluded: chain D residue 949 ASP Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1019 GLU 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 1014 THR Chi-restraints excluded: chain E residue 1019 GLU Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 949 ASP Chi-restraints excluded: chain F residue 996 GLN 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 279 optimal weight: 0.3980 chunk 450 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 312 optimal weight: 0.1980 chunk 472 optimal weight: 9.9990 chunk 434 optimal weight: 0.6980 chunk 376 optimal weight: 3.9990 chunk 39 optimal weight: 0.0270 chunk 290 optimal weight: 0.9980 chunk 230 optimal weight: 8.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 39102 Z= 0.144 Angle : 0.558 10.982 52782 Z= 0.270 Chirality : 0.037 0.162 6000 Planarity : 0.004 0.072 6570 Dihedral : 6.570 137.687 5244 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.32 % Allowed : 12.64 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4686 helix: 1.62 (0.11), residues: 2424 sheet: -0.86 (0.22), residues: 630 loop : 0.17 (0.17), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 959 HIS 0.003 0.000 HIS F 492 PHE 0.016 0.001 PHE B 568 TYR 0.025 0.001 TYR B 591 ARG 0.011 0.000 ARG D 252 ********************** 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 279 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 222 time to evaluate : 4.140 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 299 PHE cc_start: 0.8725 (m-80) cc_final: 0.8485 (m-80) REVERT: A 987 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: A 988 MET cc_start: 0.8769 (mtp) cc_final: 0.8537 (ptp) REVERT: B 254 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: B 277 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (mmt) REVERT: C 405 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 426 MET cc_start: 0.8049 (ttm) cc_final: 0.7825 (ttp) REVERT: C 632 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: C 1019 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: D 299 PHE cc_start: 0.8697 (m-80) cc_final: 0.8442 (m-80) REVERT: D 987 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: D 988 MET cc_start: 0.8769 (mtp) cc_final: 0.8537 (ptp) REVERT: E 277 MET cc_start: 0.8510 (mmt) cc_final: 0.8301 (mmt) REVERT: F 277 MET cc_start: 0.8569 (mmt) cc_final: 0.8347 (mmt) REVERT: F 405 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8819 (mm) REVERT: F 426 MET cc_start: 0.8061 (ttm) cc_final: 0.7837 (ttp) REVERT: F 632 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: F 1019 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8753 (mp0) outliers start: 57 outliers final: 36 residues processed: 262 average time/residue: 0.4890 time to fit residues: 210.6888 Evaluate side-chains 255 residues out of total 4326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 4.033 ------------------------------------------------------------------------------- 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 592 LEU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 987 MET Chi-restraints excluded: chain A residue 996 GLN Chi-restraints excluded: chain A residue 1014 THR Chi-restraints excluded: chain A residue 1019 GLU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain B residue 254 ASP 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 1014 THR Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 632 TYR Chi-restraints excluded: chain C residue 932 LEU Chi-restraints excluded: chain C residue 949 ASP 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 592 LEU Chi-restraints excluded: chain D residue 949 ASP Chi-restraints excluded: chain D residue 987 MET Chi-restraints excluded: chain D residue 996 GLN Chi-restraints excluded: chain D residue 1014 THR Chi-restraints excluded: chain D residue 1019 GLU 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 1014 THR Chi-restraints excluded: chain E residue 1031 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 632 TYR Chi-restraints excluded: chain F residue 932 LEU Chi-restraints excluded: chain F residue 949 ASP 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 298 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 346 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 376 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 386 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.078966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055678 restraints weight = 146655.259| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.46 r_work: 0.2995 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 39102 Z= 0.218 Angle : 0.574 11.436 52782 Z= 0.279 Chirality : 0.038 0.196 6000 Planarity : 0.004 0.074 6570 Dihedral : 6.539 136.799 5244 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.37 % Allowed : 12.64 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4686 helix: 1.55 (0.11), residues: 2448 sheet: -0.87 (0.22), residues: 630 loop : 0.09 (0.17), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 959 HIS 0.003 0.001 HIS D 220 PHE 0.014 0.001 PHE A 568 TYR 0.023 0.001 TYR B 591 ARG 0.007 0.000 ARG D 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6647.62 seconds wall clock time: 124 minutes 7.79 seconds (7447.79 seconds total)