Starting phenix.real_space_refine on Thu Feb 22 12:24:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nd7_12278/02_2024/7nd7_12278.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4620 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 18767 2.51 5 N 4858 2.21 5 O 5828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29591 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.37, per 1000 atoms: 0.52 Number of scatterers: 29591 At special positions: 0 Unit cell: (139.4, 137.76, 198.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5828 8.00 N 4858 7.00 C 18767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG Y 1 " - " FUC Y 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Z 1 " - " FUC Z 3 " " NAG a 1 " - " FUC a 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN H 59 " " NAG Z 1 " - " ASN F 59 " " NAG a 1 " - " ASN J 59 " Time building additional restraints: 12.50 Conformation dependent library (CDL) restraints added in 5.5 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6858 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 63 sheets defined 23.0% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.848A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.404A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.631A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.686A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.138A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.886A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.101A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.834A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.694A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.102A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.650A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.821A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.401A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.700A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.153A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.896A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.655A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.090A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.611A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.007A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.122A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.164A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.742A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.228A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.672A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.267A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.128A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.898A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.642A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.622A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.614A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.136A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.185A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.698A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.280A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.848A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.697A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.619A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 52 removed outlier: 7.026A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.215A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.714A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.257A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.249A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.564A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.536A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.639A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.662A pdb=" N TYR H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.957A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET H 100 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE H 109 " --> pdb=" O MET H 100 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.504A pdb=" N ALA L 86 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.724A pdb=" N TYR F 33 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.984A pdb=" N TYR F 111 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET F 100 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE F 109 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.178A pdb=" N GLN G 39 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU G 48 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 9 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AG4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.710A pdb=" N TYR J 33 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.974A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N MET J 100 " --> pdb=" O PHE J 109 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE J 109 " --> pdb=" O MET J 100 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 9 through 12 removed outlier: 6.170A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AG9, first strand: chain 'K' and resid 18 through 23 1237 hydrogen bonds defined for protein. 3294 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: 14.45 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9406 1.35 - 1.47: 7716 1.47 - 1.59: 12942 1.59 - 1.71: 1 1.71 - 1.83: 183 Bond restraints: 30248 Sorted by residual: bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG W 2 " pdb=" O5 NAG W 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 30243 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 881 106.72 - 113.54: 16767 113.54 - 120.37: 10653 120.37 - 127.19: 12555 127.19 - 134.01: 281 Bond angle restraints: 41137 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 110.33 14.67 4.10e+00 5.95e-02 1.28e+01 angle pdb=" C VAL K 53 " pdb=" N SER K 54 " pdb=" CA SER K 54 " ideal model delta sigma weight residual 121.99 116.76 5.23 1.56e+00 4.11e-01 1.12e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 119.73 -5.83 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA TYR A 904 " pdb=" CB TYR A 904 " pdb=" CG TYR A 904 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 121.79 -7.39 2.30e+00 1.89e-01 1.03e+01 ... (remaining 41132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 17771 17.54 - 35.09: 736 35.09 - 52.63: 161 52.63 - 70.18: 76 70.18 - 87.72: 30 Dihedral angle restraints: 18774 sinusoidal: 8076 harmonic: 10698 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.83 82.83 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.56 82.56 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -168.39 82.39 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 18771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3691 0.049 - 0.099: 843 0.099 - 0.148: 277 0.148 - 0.197: 3 0.197 - 0.247: 9 Chirality restraints: 4823 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN F 59 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU K 52 " pdb=" N GLU K 52 " pdb=" C GLU K 52 " pdb=" CB GLU K 52 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 4820 not shown) Planarity restraints: 5273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.107 5.00e-02 4.00e+02 1.64e-01 4.29e+01 pdb=" N PRO C 527 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.058 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO B 527 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 881 " 0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C THR A 881 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 881 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 882 " 0.020 2.00e-02 2.50e+03 ... (remaining 5270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4376 2.76 - 3.30: 27242 3.30 - 3.83: 49572 3.83 - 4.37: 58626 4.37 - 4.90: 101890 Nonbonded interactions: 241706 Sorted by model distance: nonbonded pdb=" O LEU B 492 " pdb=" ND2 ASN F 54 " model vdw 2.229 2.520 nonbonded pdb=" OG SER B1123 " pdb=" OD1 ASN C 914 " model vdw 2.270 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OD1 ASN B 914 " model vdw 2.298 2.440 nonbonded pdb=" O LEU C 492 " pdb=" ND2 ASN J 54 " model vdw 2.302 2.520 nonbonded pdb=" O LEU A 492 " pdb=" ND2 ASN H 54 " model vdw 2.304 2.520 ... (remaining 241701 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' and (resid 27 through 1147 or resid 1301 through 1308)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.030 Extract box with map and model: 6.360 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 83.680 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.390 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 0.097 30248 Z= 0.242 Angle : 0.632 14.667 41137 Z= 0.344 Chirality : 0.046 0.247 4823 Planarity : 0.004 0.164 5230 Dihedral : 11.283 87.722 11781 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 0.38 % Allowed : 2.19 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 3639 helix: 0.18 (0.18), residues: 711 sheet: 0.10 (0.15), residues: 1041 loop : -0.15 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 50 HIS 0.007 0.001 HIS B 519 PHE 0.020 0.001 PHE B 329 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 757 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.8615 (mt) cc_final: 0.8056 (mp) REVERT: A 392 PHE cc_start: 0.7065 (m-80) cc_final: 0.6830 (m-80) REVERT: A 513 LEU cc_start: 0.8680 (mt) cc_final: 0.8451 (mp) REVERT: A 902 MET cc_start: 0.7829 (mmm) cc_final: 0.7053 (mmm) REVERT: A 904 TYR cc_start: 0.5283 (m-10) cc_final: 0.4918 (m-10) REVERT: A 1037 SER cc_start: 0.7037 (t) cc_final: 0.6807 (t) REVERT: B 88 ASP cc_start: 0.8350 (m-30) cc_final: 0.8134 (t0) REVERT: B 269 TYR cc_start: 0.6673 (m-80) cc_final: 0.6394 (m-80) REVERT: B 490 PHE cc_start: 0.8061 (t80) cc_final: 0.7199 (t80) REVERT: B 492 LEU cc_start: 0.8762 (mt) cc_final: 0.8408 (mt) REVERT: B 513 LEU cc_start: 0.8869 (mt) cc_final: 0.8633 (mp) REVERT: B 756 TYR cc_start: 0.8622 (m-80) cc_final: 0.8135 (m-80) REVERT: B 1029 MET cc_start: 0.8235 (tpp) cc_final: 0.7960 (tpp) REVERT: C 54 LEU cc_start: 0.8581 (mt) cc_final: 0.8037 (mt) REVERT: C 92 PHE cc_start: 0.6167 (t80) cc_final: 0.5166 (t80) REVERT: C 396 TYR cc_start: 0.5856 (m-80) cc_final: 0.4688 (m-10) REVERT: C 398 ASP cc_start: 0.6748 (m-30) cc_final: 0.6452 (m-30) REVERT: C 902 MET cc_start: 0.7392 (mmm) cc_final: 0.6623 (mmm) REVERT: H 76 ILE cc_start: 0.8989 (pt) cc_final: 0.8742 (pt) outliers start: 12 outliers final: 0 residues processed: 767 average time/residue: 0.4371 time to fit residues: 522.8553 Evaluate side-chains 387 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 8.9990 chunk 277 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 332 optimal weight: 20.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 804 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN B1010 GLN B1011 GLN C 321 GLN C 762 GLN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C1010 GLN C1106 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 30248 Z= 0.267 Angle : 0.648 10.795 41137 Z= 0.333 Chirality : 0.046 0.211 4823 Planarity : 0.005 0.147 5230 Dihedral : 6.584 55.970 5295 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 8.89 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 3639 helix: 1.51 (0.20), residues: 702 sheet: 0.41 (0.15), residues: 1020 loop : -0.10 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.008 0.001 HIS J 35 PHE 0.045 0.002 PHE J 109 TYR 0.028 0.002 TYR F 60 ARG 0.007 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 424 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 269 TYR cc_start: 0.6915 (m-80) cc_final: 0.6681 (m-80) REVERT: A 492 LEU cc_start: 0.8943 (mt) cc_final: 0.8617 (tp) REVERT: A 606 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7939 (t0) REVERT: A 902 MET cc_start: 0.7801 (mmm) cc_final: 0.6999 (mmm) REVERT: A 904 TYR cc_start: 0.5316 (m-10) cc_final: 0.5065 (m-10) REVERT: A 1037 SER cc_start: 0.7468 (t) cc_final: 0.7207 (t) REVERT: B 490 PHE cc_start: 0.8004 (t80) cc_final: 0.7241 (t80) REVERT: B 492 LEU cc_start: 0.8854 (mt) cc_final: 0.8384 (mm) REVERT: B 606 ASN cc_start: 0.8241 (t0) cc_final: 0.7488 (t0) REVERT: B 756 TYR cc_start: 0.8789 (m-80) cc_final: 0.8126 (m-80) REVERT: B 1029 MET cc_start: 0.8407 (tpp) cc_final: 0.8182 (tpp) REVERT: C 42 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8760 (m) REVERT: C 54 LEU cc_start: 0.8404 (mt) cc_final: 0.8182 (mt) REVERT: C 425 LEU cc_start: 0.8536 (mp) cc_final: 0.8323 (mp) REVERT: C 606 ASN cc_start: 0.8223 (m-40) cc_final: 0.7992 (t0) REVERT: C 739 THR cc_start: 0.7603 (m) cc_final: 0.6993 (p) REVERT: C 902 MET cc_start: 0.7302 (mmm) cc_final: 0.6727 (mmm) REVERT: H 70 MET cc_start: -0.0347 (mtt) cc_final: -0.0932 (mtt) REVERT: H 102 PHE cc_start: 0.7168 (t80) cc_final: 0.6766 (t80) REVERT: F 73 ASP cc_start: 0.7164 (t0) cc_final: 0.6775 (t0) REVERT: J 70 MET cc_start: 0.2644 (mtt) cc_final: 0.0909 (mtt) REVERT: J 73 ASP cc_start: 0.7342 (t0) cc_final: 0.6955 (t0) outliers start: 79 outliers final: 41 residues processed: 483 average time/residue: 0.4381 time to fit residues: 330.9228 Evaluate side-chains 380 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 337 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 332 optimal weight: 0.0770 chunk 359 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 330 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 0.0010 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 872 GLN C 493 GLN C 787 GLN C 804 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30248 Z= 0.192 Angle : 0.598 9.196 41137 Z= 0.304 Chirality : 0.045 0.292 4823 Planarity : 0.004 0.128 5230 Dihedral : 6.036 58.418 5295 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 11.02 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3639 helix: 1.79 (0.21), residues: 693 sheet: 0.32 (0.15), residues: 1068 loop : -0.10 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 104 HIS 0.007 0.001 HIS F 35 PHE 0.020 0.001 PHE F 109 TYR 0.026 0.002 TYR H 60 ARG 0.007 0.001 ARG G 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 365 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 492 LEU cc_start: 0.9006 (mt) cc_final: 0.8732 (tp) REVERT: A 606 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.7971 (t0) REVERT: A 902 MET cc_start: 0.7767 (mmm) cc_final: 0.7004 (mmm) REVERT: A 1037 SER cc_start: 0.7475 (t) cc_final: 0.7216 (t) REVERT: B 90 VAL cc_start: 0.8078 (m) cc_final: 0.7773 (t) REVERT: B 269 TYR cc_start: 0.7101 (m-80) cc_final: 0.6847 (m-80) REVERT: B 291 CYS cc_start: 0.6298 (m) cc_final: 0.6040 (m) REVERT: B 357 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7585 (ttp80) REVERT: B 490 PHE cc_start: 0.7983 (t80) cc_final: 0.7241 (t80) REVERT: B 492 LEU cc_start: 0.8840 (mt) cc_final: 0.8421 (mm) REVERT: B 606 ASN cc_start: 0.8293 (t0) cc_final: 0.7553 (t0) REVERT: B 756 TYR cc_start: 0.8784 (m-80) cc_final: 0.8159 (m-80) REVERT: C 42 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8733 (m) REVERT: C 189 LEU cc_start: 0.8130 (tp) cc_final: 0.7872 (tt) REVERT: C 291 CYS cc_start: 0.6236 (m) cc_final: 0.5961 (m) REVERT: C 332 ILE cc_start: 0.7468 (mp) cc_final: 0.7170 (tp) REVERT: C 606 ASN cc_start: 0.8210 (m-40) cc_final: 0.7972 (t0) REVERT: C 804 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: C 902 MET cc_start: 0.7189 (mmm) cc_final: 0.6344 (mmm) REVERT: F 73 ASP cc_start: 0.7781 (t0) cc_final: 0.7527 (t0) REVERT: G 3 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5230 (p) REVERT: J 73 ASP cc_start: 0.7587 (t0) cc_final: 0.7309 (t0) REVERT: K 38 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.2870 (t80) REVERT: K 41 HIS cc_start: 0.5674 (OUTLIER) cc_final: 0.5147 (m90) outliers start: 73 outliers final: 37 residues processed: 420 average time/residue: 0.4155 time to fit residues: 278.1728 Evaluate side-chains 370 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 327 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 41 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 334 optimal weight: 0.9990 chunk 353 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 316 optimal weight: 0.0070 chunk 95 optimal weight: 0.5980 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN C 52 GLN C 450 ASN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30248 Z= 0.273 Angle : 0.609 9.985 41137 Z= 0.308 Chirality : 0.045 0.262 4823 Planarity : 0.004 0.051 5230 Dihedral : 5.746 55.362 5295 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.72 % Allowed : 12.43 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3639 helix: 1.56 (0.20), residues: 711 sheet: 0.31 (0.15), residues: 1062 loop : -0.06 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.009 0.001 HIS H 35 PHE 0.017 0.002 PHE B1089 TYR 0.019 0.002 TYR A1067 ARG 0.008 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 345 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8290 (p) cc_final: 0.7904 (t) REVERT: A 492 LEU cc_start: 0.8725 (mt) cc_final: 0.8493 (mm) REVERT: A 606 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 902 MET cc_start: 0.8100 (mmm) cc_final: 0.7305 (mmm) REVERT: A 1037 SER cc_start: 0.7794 (t) cc_final: 0.7531 (t) REVERT: B 88 ASP cc_start: 0.7958 (t0) cc_final: 0.7593 (t0) REVERT: B 90 VAL cc_start: 0.8084 (m) cc_final: 0.7832 (t) REVERT: B 269 TYR cc_start: 0.7156 (m-80) cc_final: 0.6790 (m-80) REVERT: B 357 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7658 (ttp80) REVERT: B 490 PHE cc_start: 0.8023 (t80) cc_final: 0.7320 (t80) REVERT: B 492 LEU cc_start: 0.8912 (mt) cc_final: 0.8529 (mm) REVERT: B 606 ASN cc_start: 0.8369 (t0) cc_final: 0.7383 (t0) REVERT: B 756 TYR cc_start: 0.8824 (m-80) cc_final: 0.8111 (m-80) REVERT: B 948 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8188 (mt) REVERT: C 189 LEU cc_start: 0.8116 (tp) cc_final: 0.7873 (tt) REVERT: C 291 CYS cc_start: 0.6557 (m) cc_final: 0.6342 (m) REVERT: C 606 ASN cc_start: 0.8282 (m-40) cc_final: 0.8054 (t0) REVERT: C 902 MET cc_start: 0.7608 (mmm) cc_final: 0.6602 (mmm) REVERT: C 948 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8276 (mt) REVERT: L 49 MET cc_start: 0.4060 (tpp) cc_final: 0.3697 (ttt) REVERT: G 3 VAL cc_start: 0.5413 (OUTLIER) cc_final: 0.5200 (p) REVERT: J 73 ASP cc_start: 0.7292 (t0) cc_final: 0.7048 (t0) REVERT: K 38 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.3323 (t80) outliers start: 87 outliers final: 61 residues processed: 408 average time/residue: 0.4253 time to fit residues: 281.7072 Evaluate side-chains 376 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 310 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 38 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 263 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 244 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 317 optimal weight: 0.0570 chunk 89 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 450 ASN C 52 GLN C 580 GLN C 804 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30248 Z= 0.198 Angle : 0.567 10.164 41137 Z= 0.286 Chirality : 0.044 0.225 4823 Planarity : 0.004 0.045 5230 Dihedral : 5.439 58.398 5295 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.28 % Allowed : 13.40 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3639 helix: 1.87 (0.21), residues: 690 sheet: 0.32 (0.15), residues: 1041 loop : -0.11 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 104 HIS 0.003 0.001 HIS C1064 PHE 0.015 0.001 PHE B 192 TYR 0.017 0.002 TYR A 265 ARG 0.007 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 338 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8725 (mt) cc_final: 0.8500 (mm) REVERT: A 606 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8042 (t0) REVERT: A 902 MET cc_start: 0.8504 (mmm) cc_final: 0.7710 (mmm) REVERT: A 1037 SER cc_start: 0.7870 (t) cc_final: 0.7556 (t) REVERT: A 1101 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.5378 (t-90) REVERT: A 1104 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 88 ASP cc_start: 0.8023 (t0) cc_final: 0.7561 (t0) REVERT: B 90 VAL cc_start: 0.8070 (m) cc_final: 0.7853 (t) REVERT: B 269 TYR cc_start: 0.7195 (m-80) cc_final: 0.6894 (m-80) REVERT: B 357 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7688 (ttp80) REVERT: B 490 PHE cc_start: 0.8017 (t80) cc_final: 0.7352 (t80) REVERT: B 492 LEU cc_start: 0.8938 (mt) cc_final: 0.8571 (mm) REVERT: B 606 ASN cc_start: 0.8360 (t0) cc_final: 0.7448 (t0) REVERT: B 756 TYR cc_start: 0.8809 (m-80) cc_final: 0.8161 (m-80) REVERT: B 948 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8130 (mt) REVERT: C 189 LEU cc_start: 0.8068 (tp) cc_final: 0.7854 (tt) REVERT: C 492 LEU cc_start: 0.8936 (mm) cc_final: 0.8680 (tp) REVERT: C 606 ASN cc_start: 0.8312 (m-40) cc_final: 0.8072 (t0) REVERT: C 948 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8251 (mt) REVERT: L 34 TYR cc_start: 0.0337 (m-80) cc_final: -0.0218 (m-80) REVERT: L 49 MET cc_start: 0.3985 (tpp) cc_final: 0.3673 (ttt) REVERT: G 3 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5141 (p) REVERT: K 41 HIS cc_start: 0.5431 (m90) cc_final: 0.4755 (m90) outliers start: 73 outliers final: 57 residues processed: 396 average time/residue: 0.4039 time to fit residues: 258.7558 Evaluate side-chains 373 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 310 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 2.9990 chunk 318 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 293 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 804 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30248 Z= 0.264 Angle : 0.599 11.631 41137 Z= 0.302 Chirality : 0.045 0.217 4823 Planarity : 0.004 0.046 5230 Dihedral : 5.339 55.331 5295 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.28 % Rotamer: Outliers : 2.82 % Allowed : 14.08 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3639 helix: 1.62 (0.21), residues: 690 sheet: 0.32 (0.16), residues: 1011 loop : -0.13 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.018 0.001 HIS A1101 PHE 0.029 0.002 PHE B 192 TYR 0.020 0.002 TYR K 38 ARG 0.008 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 308 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 606 ASN cc_start: 0.8583 (t0) cc_final: 0.8099 (t0) REVERT: A 902 MET cc_start: 0.8624 (mmm) cc_final: 0.7590 (mmm) REVERT: A 1037 SER cc_start: 0.8027 (t) cc_final: 0.7718 (t) REVERT: A 1104 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8599 (p) REVERT: B 88 ASP cc_start: 0.8153 (t0) cc_final: 0.7669 (t0) REVERT: B 90 VAL cc_start: 0.8071 (m) cc_final: 0.7796 (t) REVERT: B 269 TYR cc_start: 0.7233 (m-80) cc_final: 0.6888 (m-80) REVERT: B 357 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7734 (ttp80) REVERT: B 490 PHE cc_start: 0.7970 (t80) cc_final: 0.7268 (t80) REVERT: B 492 LEU cc_start: 0.8764 (mt) cc_final: 0.8349 (mm) REVERT: B 606 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7569 (t0) REVERT: B 756 TYR cc_start: 0.8853 (m-80) cc_final: 0.8184 (m-80) REVERT: B 804 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: B 948 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 231 ILE cc_start: 0.7786 (mm) cc_final: 0.7506 (tt) REVERT: C 492 LEU cc_start: 0.9020 (mm) cc_final: 0.8742 (tp) REVERT: C 606 ASN cc_start: 0.8341 (m-40) cc_final: 0.8098 (t0) REVERT: C 902 MET cc_start: 0.7782 (mmm) cc_final: 0.7048 (mmm) REVERT: C 948 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8312 (mt) REVERT: L 34 TYR cc_start: 0.0310 (m-80) cc_final: -0.0244 (m-80) REVERT: L 49 MET cc_start: 0.4673 (tpp) cc_final: 0.3901 (ttm) REVERT: G 3 VAL cc_start: 0.5452 (OUTLIER) cc_final: 0.5152 (p) REVERT: G 41 HIS cc_start: 0.6434 (OUTLIER) cc_final: 0.5941 (m90) REVERT: K 41 HIS cc_start: 0.5269 (m90) cc_final: 0.4882 (m90) outliers start: 90 outliers final: 72 residues processed: 379 average time/residue: 0.4086 time to fit residues: 249.8048 Evaluate side-chains 380 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 301 time to evaluate : 3.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 9.9990 chunk 39 optimal weight: 0.0470 chunk 201 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 352 optimal weight: 0.8980 chunk 220 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN L 40 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30248 Z= 0.195 Angle : 0.571 11.035 41137 Z= 0.286 Chirality : 0.044 0.250 4823 Planarity : 0.003 0.047 5230 Dihedral : 5.160 54.541 5295 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 2.91 % Allowed : 14.55 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3639 helix: 1.70 (0.21), residues: 690 sheet: 0.35 (0.16), residues: 1014 loop : -0.13 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.003 0.001 HIS A1064 PHE 0.015 0.001 PHE A 515 TYR 0.019 0.001 TYR F 111 ARG 0.006 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 303 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 88 ASP cc_start: 0.8179 (t0) cc_final: 0.7723 (t0) REVERT: A 606 ASN cc_start: 0.8575 (t0) cc_final: 0.8103 (t0) REVERT: A 902 MET cc_start: 0.8608 (mmm) cc_final: 0.7560 (mmm) REVERT: A 1037 SER cc_start: 0.8019 (t) cc_final: 0.7718 (t) REVERT: A 1104 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 88 ASP cc_start: 0.8112 (t0) cc_final: 0.7549 (t0) REVERT: B 90 VAL cc_start: 0.8073 (m) cc_final: 0.7815 (t) REVERT: B 357 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7644 (ttp80) REVERT: B 490 PHE cc_start: 0.7970 (t80) cc_final: 0.7284 (t80) REVERT: B 492 LEU cc_start: 0.8774 (mt) cc_final: 0.8361 (mm) REVERT: B 606 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7551 (t0) REVERT: B 756 TYR cc_start: 0.8830 (m-80) cc_final: 0.8182 (m-80) REVERT: B 948 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8097 (mt) REVERT: C 231 ILE cc_start: 0.7813 (mm) cc_final: 0.7576 (tt) REVERT: C 492 LEU cc_start: 0.9023 (mm) cc_final: 0.8724 (tp) REVERT: C 606 ASN cc_start: 0.8326 (m-40) cc_final: 0.8075 (t0) REVERT: C 902 MET cc_start: 0.7763 (mmm) cc_final: 0.7013 (mmm) REVERT: C 948 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8069 (mt) REVERT: L 34 TYR cc_start: 0.0735 (m-80) cc_final: 0.0302 (m-80) REVERT: G 3 VAL cc_start: 0.5439 (OUTLIER) cc_final: 0.5154 (p) REVERT: G 41 HIS cc_start: 0.6262 (m-70) cc_final: 0.5888 (m90) REVERT: K 38 TYR cc_start: 0.3178 (OUTLIER) cc_final: 0.2672 (t80) outliers start: 93 outliers final: 76 residues processed: 377 average time/residue: 0.4126 time to fit residues: 252.8692 Evaluate side-chains 373 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 291 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 224 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B1005 GLN C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30248 Z= 0.222 Angle : 0.575 11.378 41137 Z= 0.288 Chirality : 0.045 0.272 4823 Planarity : 0.004 0.069 5230 Dihedral : 5.097 54.340 5295 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 14.68 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3639 helix: 1.51 (0.20), residues: 708 sheet: 0.31 (0.16), residues: 1020 loop : -0.08 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.004 0.001 HIS B1064 PHE 0.040 0.001 PHE C 392 TYR 0.018 0.001 TYR G 88 ARG 0.005 0.000 ARG K 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 296 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8146 (t0) cc_final: 0.7707 (t0) REVERT: A 606 ASN cc_start: 0.8596 (t0) cc_final: 0.8133 (t0) REVERT: A 902 MET cc_start: 0.8642 (mmm) cc_final: 0.7540 (mmm) REVERT: B 88 ASP cc_start: 0.8104 (t0) cc_final: 0.7591 (t0) REVERT: B 90 VAL cc_start: 0.8079 (m) cc_final: 0.7811 (t) REVERT: B 291 CYS cc_start: 0.6740 (m) cc_final: 0.6393 (m) REVERT: B 357 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7576 (ttp80) REVERT: B 490 PHE cc_start: 0.7999 (t80) cc_final: 0.7332 (t80) REVERT: B 492 LEU cc_start: 0.8790 (mt) cc_final: 0.8404 (mm) REVERT: B 606 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7596 (t0) REVERT: B 948 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8109 (mt) REVERT: C 231 ILE cc_start: 0.7818 (mm) cc_final: 0.7602 (tt) REVERT: C 291 CYS cc_start: 0.6696 (m) cc_final: 0.6274 (m) REVERT: C 492 LEU cc_start: 0.9039 (mm) cc_final: 0.8741 (tp) REVERT: C 606 ASN cc_start: 0.8342 (m-40) cc_final: 0.8088 (t0) REVERT: C 902 MET cc_start: 0.7753 (mmm) cc_final: 0.6889 (mmm) REVERT: C 948 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8123 (mt) REVERT: L 34 TYR cc_start: 0.0692 (m-80) cc_final: 0.0259 (m-80) REVERT: G 3 VAL cc_start: 0.5437 (OUTLIER) cc_final: 0.5178 (p) REVERT: K 38 TYR cc_start: 0.3537 (OUTLIER) cc_final: 0.3118 (t80) REVERT: K 41 HIS cc_start: 0.5321 (m90) cc_final: 0.5001 (m-70) outliers start: 101 outliers final: 82 residues processed: 371 average time/residue: 0.3994 time to fit residues: 240.6103 Evaluate side-chains 372 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 285 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 89 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 1.9990 chunk 308 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 143 optimal weight: 0.0770 chunk 258 optimal weight: 0.0070 chunk 100 optimal weight: 10.0000 chunk 297 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 784 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 613 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30248 Z= 0.180 Angle : 0.568 12.589 41137 Z= 0.285 Chirality : 0.044 0.258 4823 Planarity : 0.004 0.050 5230 Dihedral : 5.008 54.639 5295 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 3.04 % Allowed : 15.02 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3639 helix: 1.62 (0.21), residues: 708 sheet: 0.34 (0.16), residues: 1017 loop : -0.07 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 104 HIS 0.003 0.001 HIS B1048 PHE 0.051 0.001 PHE C 392 TYR 0.020 0.001 TYR B 369 ARG 0.007 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 300 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8181 (t0) cc_final: 0.7702 (t0) REVERT: A 606 ASN cc_start: 0.8552 (t0) cc_final: 0.8121 (t0) REVERT: A 902 MET cc_start: 0.8622 (mmm) cc_final: 0.7539 (mmm) REVERT: B 88 ASP cc_start: 0.8227 (t0) cc_final: 0.7672 (t0) REVERT: B 90 VAL cc_start: 0.8039 (m) cc_final: 0.7763 (t) REVERT: B 291 CYS cc_start: 0.7055 (m) cc_final: 0.6448 (m) REVERT: B 357 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7529 (ttp80) REVERT: B 490 PHE cc_start: 0.8032 (t80) cc_final: 0.7399 (t80) REVERT: B 492 LEU cc_start: 0.8794 (mt) cc_final: 0.8403 (mm) REVERT: B 606 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7746 (t0) REVERT: B 756 TYR cc_start: 0.8851 (m-80) cc_final: 0.8244 (m-80) REVERT: B 948 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (mt) REVERT: C 291 CYS cc_start: 0.6711 (m) cc_final: 0.6292 (m) REVERT: C 492 LEU cc_start: 0.8899 (mm) cc_final: 0.8621 (tp) REVERT: C 606 ASN cc_start: 0.8333 (m-40) cc_final: 0.8076 (t0) REVERT: C 902 MET cc_start: 0.7746 (mmm) cc_final: 0.6928 (mmm) REVERT: C 948 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (mt) REVERT: L 34 TYR cc_start: 0.0617 (m-80) cc_final: 0.0197 (m-80) REVERT: L 49 MET cc_start: 0.3534 (tpp) cc_final: 0.3256 (tpt) REVERT: F 81 MET cc_start: 0.6719 (mmm) cc_final: 0.6320 (mmt) REVERT: G 3 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5198 (p) REVERT: K 38 TYR cc_start: 0.3526 (OUTLIER) cc_final: 0.2982 (t80) REVERT: K 41 HIS cc_start: 0.5103 (m90) cc_final: 0.4744 (m-70) outliers start: 97 outliers final: 75 residues processed: 372 average time/residue: 0.4085 time to fit residues: 246.0438 Evaluate side-chains 363 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 283 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 89 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 6.9990 chunk 347 optimal weight: 20.0000 chunk 212 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 364 optimal weight: 30.0000 chunk 335 optimal weight: 1.9990 chunk 290 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1005 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 30248 Z= 0.257 Angle : 0.835 59.200 41137 Z= 0.477 Chirality : 0.045 0.478 4823 Planarity : 0.004 0.102 5230 Dihedral : 5.004 54.624 5295 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 2.75 % Allowed : 15.65 % Favored : 81.60 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3639 helix: 1.60 (0.21), residues: 708 sheet: 0.35 (0.16), residues: 1017 loop : -0.07 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 104 HIS 0.052 0.001 HIS A 207 PHE 0.041 0.001 PHE C 392 TYR 0.045 0.001 TYR K 88 ARG 0.020 0.000 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 284 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8195 (t0) cc_final: 0.7704 (t0) REVERT: A 606 ASN cc_start: 0.8559 (t0) cc_final: 0.8124 (t0) REVERT: A 902 MET cc_start: 0.8631 (mmm) cc_final: 0.7538 (mmm) REVERT: B 88 ASP cc_start: 0.8225 (t0) cc_final: 0.7675 (t0) REVERT: B 90 VAL cc_start: 0.8041 (m) cc_final: 0.7769 (t) REVERT: B 291 CYS cc_start: 0.7065 (m) cc_final: 0.6668 (m) REVERT: B 357 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7581 (ttp80) REVERT: B 490 PHE cc_start: 0.8037 (t80) cc_final: 0.7401 (t80) REVERT: B 492 LEU cc_start: 0.8791 (mt) cc_final: 0.8405 (mm) REVERT: B 606 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7750 (t0) REVERT: B 756 TYR cc_start: 0.8854 (m-80) cc_final: 0.8242 (m-80) REVERT: B 948 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8001 (mt) REVERT: C 291 CYS cc_start: 0.6730 (m) cc_final: 0.6299 (m) REVERT: C 492 LEU cc_start: 0.8903 (mm) cc_final: 0.8619 (tp) REVERT: C 606 ASN cc_start: 0.8339 (m-40) cc_final: 0.8078 (t0) REVERT: C 902 MET cc_start: 0.7755 (mmm) cc_final: 0.6910 (mmm) REVERT: C 948 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8247 (mt) REVERT: L 34 TYR cc_start: 0.0618 (m-80) cc_final: 0.0133 (m-80) REVERT: L 49 MET cc_start: 0.3596 (tpp) cc_final: 0.3280 (tpt) REVERT: G 3 VAL cc_start: 0.5460 (OUTLIER) cc_final: 0.5200 (p) REVERT: K 38 TYR cc_start: 0.3317 (OUTLIER) cc_final: 0.3038 (t80) REVERT: K 41 HIS cc_start: 0.5103 (m90) cc_final: 0.4741 (m-70) outliers start: 88 outliers final: 80 residues processed: 348 average time/residue: 0.4024 time to fit residues: 227.0650 Evaluate side-chains 369 residues out of total 3195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 284 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 104 MET Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 38 TYR Chi-restraints excluded: chain K residue 89 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.9990 chunk 309 optimal weight: 20.0000 chunk 88 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 290 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A1005 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.183770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.144866 restraints weight = 57059.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.142283 restraints weight = 77900.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.143795 restraints weight = 70304.564| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 30248 Z= 0.277 Angle : 0.935 59.175 41137 Z= 0.547 Chirality : 0.044 0.276 4823 Planarity : 0.005 0.136 5230 Dihedral : 5.000 54.619 5295 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 2.66 % Allowed : 15.65 % Favored : 81.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3639 helix: 1.59 (0.21), residues: 708 sheet: 0.35 (0.16), residues: 1017 loop : -0.07 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 104 HIS 0.045 0.001 HIS A 207 PHE 0.035 0.001 PHE C 392 TYR 0.039 0.001 TYR K 88 ARG 0.017 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6061.95 seconds wall clock time: 111 minutes 48.61 seconds (6708.61 seconds total)