Starting phenix.real_space_refine on Mon Feb 19 09:36:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlx_27519/02_2024/8dlx_27519.pdb" } resolution = 2.45 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 15445 2.51 5 N 3979 2.21 5 O 4763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "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: 24293 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7838 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 53, 'TRANS': 949} Chain breaks: 8 Chain: "B" Number of atoms: 6571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6571 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 45, 'TRANS': 797} Chain breaks: 8 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} 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: "F" 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: "G" 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: "J" 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: "K" 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: "L" 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: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 12.63, per 1000 atoms: 0.52 Number of scatterers: 24293 At special positions: 0 Unit cell: (137, 146, 182, 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 106 16.00 O 4763 8.00 N 3979 7.00 C 15445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.03 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 15 " - pdb=" SG CYS B 136 " 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 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=2.03 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 15 " - pdb=" SG CYS C 136 " 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=2.03 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 95 " distance=2.04 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 17 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 17 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 4.4 seconds 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 39 sheets defined 24.9% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 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 370 removed outlier: 3.844A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.526A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.436A 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 616 through 620 removed outlier: 4.085A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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: 3.633A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.926A 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 945 through 965 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.050A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.548A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.960A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.558A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.916A 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 945 through 965 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.737A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.577A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (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 365 through 370 removed outlier: 3.518A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.113A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.344A 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 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 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: 3.654A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.957A 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 945 through 965 removed outlier: 3.548A 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 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.305A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.545A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.512A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 86 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 78 through 79 current: chain 'A' and resid 188 through 197 removed outlier: 6.414A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.506A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.214A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.691A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.829A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.727A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.850A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.279A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.740A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 78 through 79 current: chain 'B' and resid 188 through 197 removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.117A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.836A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.786A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.620A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.959A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.461A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.885A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.323A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC8, first strand: chain 'C' and resid 27 through 30 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 188 through 197 removed outlier: 6.425A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.120A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.044A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.459A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.246A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.250A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.674A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.821A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.206A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.261A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.944A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 901 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.82 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7448 1.34 - 1.46: 6228 1.46 - 1.59: 11015 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 24827 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.84e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 ... (remaining 24822 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.46: 436 104.46 - 111.86: 11814 111.86 - 119.26: 8397 119.26 - 126.66: 12862 126.66 - 134.06: 282 Bond angle restraints: 33791 Sorted by residual: angle pdb=" CB ARG A 357 " pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " ideal model delta sigma weight residual 111.30 100.16 11.14 2.30e+00 1.89e-01 2.35e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.46 -5.76 1.22e+00 6.72e-01 2.23e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.19 -5.49 1.22e+00 6.72e-01 2.03e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.14 -5.44 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" C PHE A 377 " ideal model delta sigma weight residual 107.37 99.25 8.12 2.07e+00 2.33e-01 1.54e+01 ... (remaining 33786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 14349 17.96 - 35.91: 956 35.91 - 53.87: 164 53.87 - 71.83: 66 71.83 - 89.78: 28 Dihedral angle restraints: 15563 sinusoidal: 6832 harmonic: 8731 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 126.41 -33.41 1 1.00e+01 1.00e-02 1.59e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -88.35 58.35 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU A1111 " pdb=" CG GLU A1111 " pdb=" CD GLU A1111 " pdb=" OE1 GLU A1111 " ideal model delta sinusoidal sigma weight residual 0.00 -89.78 89.78 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 15560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3349 0.077 - 0.155: 625 0.155 - 0.232: 39 0.232 - 0.309: 5 0.309 - 0.386: 2 Chirality restraints: 4020 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4017 not shown) Planarity restraints: 4335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 486 " -0.042 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE C 486 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE C 486 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 486 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 486 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE C 486 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE C 486 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 99 " 0.035 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP H 99 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP H 99 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP H 99 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 99 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 99 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 99 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 99 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C MET C 902 " 0.042 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 ... (remaining 4332 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6289 2.80 - 3.33: 20555 3.33 - 3.85: 41617 3.85 - 4.38: 47881 4.38 - 4.90: 82315 Nonbonded interactions: 198657 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.279 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.294 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.298 2.440 ... (remaining 198652 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 'C' and (resid 14 through 455 or resid 493 through 1147 or resid 1301 thr \ ough 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.930 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 65.420 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.280 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.005 0.102 24827 Z= 0.331 Angle : 0.832 11.143 33791 Z= 0.450 Chirality : 0.056 0.386 4020 Planarity : 0.006 0.060 4294 Dihedral : 13.112 89.782 9825 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % 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: -0.13 (0.14), residues: 2951 helix: 1.04 (0.18), residues: 631 sheet: 0.45 (0.18), residues: 718 loop : -0.79 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP H 99 HIS 0.013 0.001 HIS H 35 PHE 0.057 0.002 PHE C 486 TYR 0.031 0.002 TYR C1067 ARG 0.014 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 PRO cc_start: 0.8927 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: B 153 MET cc_start: 0.6723 (mpp) cc_final: 0.6130 (tpt) REVERT: B 198 ASP cc_start: 0.8227 (m-30) cc_final: 0.7706 (p0) REVERT: B 200 TYR cc_start: 0.8560 (m-10) cc_final: 0.7871 (m-80) REVERT: B 238 PHE cc_start: 0.6740 (p90) cc_final: 0.6443 (p90) REVERT: B 240 THR cc_start: 0.7167 (m) cc_final: 0.6891 (t) REVERT: B 990 GLU cc_start: 0.8218 (tt0) cc_final: 0.7880 (tm-30) REVERT: B 1029 MET cc_start: 0.9370 (tpp) cc_final: 0.9105 (tpp) REVERT: C 97 LYS cc_start: 0.8354 (pttt) cc_final: 0.7817 (tptp) REVERT: C 421 TYR cc_start: 0.9025 (m-80) cc_final: 0.8616 (m-10) REVERT: H 34 MET cc_start: 0.7333 (mmm) cc_final: 0.6735 (mmt) REVERT: H 48 ILE cc_start: 0.8035 (mt) cc_final: 0.7617 (mt) REVERT: H 79 TYR cc_start: 0.8198 (m-10) cc_final: 0.7981 (m-80) REVERT: H 100 LEU cc_start: 0.8291 (mt) cc_final: 0.8007 (mp) REVERT: H 101 TYR cc_start: 0.8567 (m-80) cc_final: 0.8327 (m-80) outliers start: 2 outliers final: 1 residues processed: 182 average time/residue: 1.2681 time to fit residues: 270.7359 Evaluate side-chains 91 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 926 GLN A1002 GLN B 218 GLN B 245 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 414 GLN C 580 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24827 Z= 0.238 Angle : 0.531 9.269 33791 Z= 0.274 Chirality : 0.044 0.386 4020 Planarity : 0.004 0.058 4294 Dihedral : 6.814 59.594 4454 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.84 % Allowed : 5.71 % Favored : 93.46 % 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: 0.41 (0.15), residues: 2951 helix: 2.03 (0.20), residues: 644 sheet: 0.48 (0.19), residues: 677 loop : -0.53 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.006 0.001 HIS B 245 PHE 0.019 0.001 PHE C 238 TYR 0.024 0.001 TYR H 94 ARG 0.006 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 2.743 Fit side-chains revert: symmetry clash REVERT: B 85 PRO cc_start: 0.8917 (Cg_exo) cc_final: 0.8448 (Cg_endo) REVERT: B 153 MET cc_start: 0.7053 (mpp) cc_final: 0.6397 (tpt) REVERT: B 198 ASP cc_start: 0.8331 (m-30) cc_final: 0.7764 (p0) REVERT: B 200 TYR cc_start: 0.8520 (m-10) cc_final: 0.7836 (m-80) REVERT: B 240 THR cc_start: 0.7209 (m) cc_final: 0.6768 (t) REVERT: B 1145 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7313 (tm) REVERT: C 97 LYS cc_start: 0.8338 (pttt) cc_final: 0.7838 (tptp) REVERT: C 421 TYR cc_start: 0.9017 (m-80) cc_final: 0.8511 (m-10) REVERT: C 740 MET cc_start: 0.8600 (tpp) cc_final: 0.8230 (tpp) REVERT: C 993 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9090 (mp) REVERT: H 34 MET cc_start: 0.6981 (mmm) cc_final: 0.6729 (tpt) REVERT: H 48 ILE cc_start: 0.7906 (mt) cc_final: 0.7705 (mp) REVERT: H 99 TRP cc_start: 0.6950 (t60) cc_final: 0.6595 (t60) outliers start: 22 outliers final: 5 residues processed: 104 average time/residue: 1.1971 time to fit residues: 148.6627 Evaluate side-chains 80 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1002 GLN B 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN C 121 ASN C 824 ASN C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24827 Z= 0.313 Angle : 0.558 11.078 33791 Z= 0.283 Chirality : 0.045 0.369 4020 Planarity : 0.004 0.060 4294 Dihedral : 6.098 59.819 4452 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.99 % Allowed : 6.77 % Favored : 92.24 % 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 (0.15), residues: 2951 helix: 2.34 (0.20), residues: 639 sheet: 0.34 (0.20), residues: 672 loop : -0.45 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.005 0.001 HIS C 519 PHE 0.018 0.002 PHE B 275 TYR 0.021 0.002 TYR C1067 ARG 0.008 0.000 ARG C 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 3.378 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: A 1010 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: B 104 TRP cc_start: 0.7893 (m100) cc_final: 0.7680 (m100) REVERT: B 153 MET cc_start: 0.7285 (mpp) cc_final: 0.6450 (tpt) REVERT: B 240 THR cc_start: 0.7220 (m) cc_final: 0.6748 (t) REVERT: B 990 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 1145 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7358 (tm) REVERT: C 334 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8542 (p0) REVERT: C 421 TYR cc_start: 0.9057 (m-80) cc_final: 0.8552 (m-10) REVERT: C 455 LEU cc_start: 0.8182 (pp) cc_final: 0.7959 (pt) REVERT: H 34 MET cc_start: 0.6727 (mmm) cc_final: 0.6387 (mmp) REVERT: H 82 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6301 (tmt) REVERT: H 99 TRP cc_start: 0.6849 (t60) cc_final: 0.6377 (t-100) outliers start: 26 outliers final: 9 residues processed: 101 average time/residue: 1.1431 time to fit residues: 140.2517 Evaluate side-chains 88 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 289 optimal weight: 0.0020 chunk 142 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 196 ASN B 901 GLN B1002 GLN C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24827 Z= 0.133 Angle : 0.471 8.247 33791 Z= 0.238 Chirality : 0.043 0.379 4020 Planarity : 0.003 0.050 4294 Dihedral : 5.465 58.956 4452 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.87 % Allowed : 8.25 % Favored : 90.87 % 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: 0.73 (0.15), residues: 2951 helix: 2.64 (0.21), residues: 640 sheet: 0.50 (0.19), residues: 694 loop : -0.40 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.005 0.000 HIS H 35 PHE 0.015 0.001 PHE C 238 TYR 0.023 0.001 TYR H 94 ARG 0.003 0.000 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7262 (mpp) cc_final: 0.6432 (tpt) REVERT: B 240 THR cc_start: 0.7138 (m) cc_final: 0.6695 (t) REVERT: B 990 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 1002 GLN cc_start: 0.8269 (tp40) cc_final: 0.8068 (tp40) REVERT: C 421 TYR cc_start: 0.9009 (m-80) cc_final: 0.8596 (m-10) REVERT: H 34 MET cc_start: 0.6636 (mmm) cc_final: 0.6350 (mmp) REVERT: H 99 TRP cc_start: 0.6837 (t60) cc_final: 0.6460 (t-100) outliers start: 23 outliers final: 7 residues processed: 92 average time/residue: 1.2960 time to fit residues: 143.8478 Evaluate side-chains 75 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 0.0980 chunk 246 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 394 ASN C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24827 Z= 0.265 Angle : 0.505 8.893 33791 Z= 0.255 Chirality : 0.044 0.363 4020 Planarity : 0.003 0.050 4294 Dihedral : 5.261 58.378 4452 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.91 % Allowed : 8.75 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2951 helix: 2.56 (0.20), residues: 646 sheet: 0.41 (0.20), residues: 627 loop : -0.39 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 104 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.001 PHE A 898 TYR 0.018 0.001 TYR C1067 ARG 0.008 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7401 (mpp) cc_final: 0.6485 (tpt) REVERT: B 990 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 1145 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7361 (tm) REVERT: C 135 PHE cc_start: 0.7056 (m-80) cc_final: 0.6488 (p90) REVERT: C 421 TYR cc_start: 0.8992 (m-80) cc_final: 0.8589 (m-10) REVERT: H 34 MET cc_start: 0.6608 (mmm) cc_final: 0.6357 (mmp) REVERT: H 82 MET cc_start: 0.6575 (tmt) cc_final: 0.6361 (tmt) REVERT: H 99 TRP cc_start: 0.6850 (t60) cc_final: 0.6414 (t-100) outliers start: 24 outliers final: 9 residues processed: 91 average time/residue: 1.2174 time to fit residues: 133.0079 Evaluate side-chains 76 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 3.9990 chunk 260 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 289 optimal weight: 20.0000 chunk 240 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24827 Z= 0.125 Angle : 0.458 8.498 33791 Z= 0.232 Chirality : 0.043 0.353 4020 Planarity : 0.003 0.042 4294 Dihedral : 4.955 57.230 4452 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.76 % Allowed : 9.13 % Favored : 90.11 % 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: 0.79 (0.15), residues: 2951 helix: 2.70 (0.21), residues: 647 sheet: 0.51 (0.20), residues: 670 loop : -0.34 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.003 0.000 HIS B 245 PHE 0.012 0.001 PHE C 238 TYR 0.015 0.001 TYR H 94 ARG 0.007 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7291 (mpp) cc_final: 0.6423 (tpt) REVERT: B 240 THR cc_start: 0.6845 (m) cc_final: 0.6389 (t) REVERT: B 245 HIS cc_start: 0.3394 (m90) cc_final: 0.1406 (t-170) REVERT: B 740 MET cc_start: 0.8728 (tpp) cc_final: 0.8368 (ttt) REVERT: B 990 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 1145 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7393 (tm) REVERT: C 421 TYR cc_start: 0.9001 (m-80) cc_final: 0.8604 (m-10) REVERT: H 82 MET cc_start: 0.6658 (tmt) cc_final: 0.6437 (tmt) REVERT: H 99 TRP cc_start: 0.6860 (t60) cc_final: 0.6511 (t60) outliers start: 20 outliers final: 10 residues processed: 88 average time/residue: 1.2443 time to fit residues: 131.7375 Evaluate side-chains 77 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 243 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 49 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24827 Z= 0.293 Angle : 0.516 8.458 33791 Z= 0.260 Chirality : 0.044 0.357 4020 Planarity : 0.003 0.042 4294 Dihedral : 5.019 56.569 4452 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.76 % Allowed : 9.43 % Favored : 89.81 % 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: 0.67 (0.15), residues: 2951 helix: 2.59 (0.20), residues: 646 sheet: 0.31 (0.20), residues: 653 loop : -0.35 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 104 HIS 0.003 0.001 HIS B 245 PHE 0.018 0.001 PHE A 898 TYR 0.020 0.001 TYR C1067 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7344 (mpp) cc_final: 0.6463 (tpt) REVERT: B 240 THR cc_start: 0.7098 (m) cc_final: 0.6694 (t) REVERT: B 740 MET cc_start: 0.8790 (tpp) cc_final: 0.8300 (ttt) REVERT: B 990 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 1145 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7344 (tm) REVERT: C 135 PHE cc_start: 0.7282 (m-80) cc_final: 0.6534 (p90) REVERT: C 421 TYR cc_start: 0.9024 (m-80) cc_final: 0.8617 (m-10) REVERT: C 740 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8353 (tmm) REVERT: H 38 ARG cc_start: 0.7036 (ppp-140) cc_final: 0.6768 (ptm-80) REVERT: H 82 MET cc_start: 0.6636 (tmt) cc_final: 0.6343 (tmt) REVERT: H 99 TRP cc_start: 0.6864 (t60) cc_final: 0.6440 (t-100) outliers start: 20 outliers final: 13 residues processed: 84 average time/residue: 1.1701 time to fit residues: 118.3518 Evaluate side-chains 78 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 196 optimal weight: 30.0000 chunk 142 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24827 Z= 0.146 Angle : 0.466 8.714 33791 Z= 0.235 Chirality : 0.043 0.353 4020 Planarity : 0.003 0.041 4294 Dihedral : 4.814 54.502 4452 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.84 % Allowed : 9.55 % Favored : 89.62 % 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: 0.75 (0.15), residues: 2951 helix: 2.74 (0.20), residues: 647 sheet: 0.33 (0.20), residues: 641 loop : -0.31 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.002 0.000 HIS B 245 PHE 0.011 0.001 PHE C 238 TYR 0.021 0.001 TYR H 94 ARG 0.005 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7186 (mpp) cc_final: 0.6384 (tpt) REVERT: B 240 THR cc_start: 0.7080 (m) cc_final: 0.6826 (t) REVERT: B 740 MET cc_start: 0.8757 (tpp) cc_final: 0.8257 (ttt) REVERT: B 990 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 1145 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7368 (tm) REVERT: C 135 PHE cc_start: 0.7242 (m-80) cc_final: 0.6479 (p90) REVERT: C 421 TYR cc_start: 0.9011 (m-80) cc_final: 0.8618 (m-10) REVERT: H 38 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6824 (ptm-80) REVERT: H 82 MET cc_start: 0.6637 (tmt) cc_final: 0.6291 (tmt) REVERT: H 99 TRP cc_start: 0.6814 (t60) cc_final: 0.6417 (t-100) outliers start: 22 outliers final: 13 residues processed: 83 average time/residue: 1.2734 time to fit residues: 126.9106 Evaluate side-chains 80 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 267 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24827 Z= 0.265 Angle : 0.503 9.104 33791 Z= 0.253 Chirality : 0.044 0.357 4020 Planarity : 0.003 0.040 4294 Dihedral : 4.885 54.406 4452 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.68 % Allowed : 9.89 % Favored : 89.43 % 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: 0.71 (0.15), residues: 2951 helix: 2.68 (0.20), residues: 646 sheet: 0.30 (0.20), residues: 662 loop : -0.34 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 104 HIS 0.002 0.001 HIS C1048 PHE 0.020 0.001 PHE A 565 TYR 0.019 0.001 TYR H 94 ARG 0.005 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7181 (mpp) cc_final: 0.6341 (tpt) REVERT: B 740 MET cc_start: 0.8804 (tpp) cc_final: 0.8222 (ttt) REVERT: B 990 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 1145 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7363 (tm) REVERT: C 135 PHE cc_start: 0.7315 (m-80) cc_final: 0.6513 (p90) REVERT: C 421 TYR cc_start: 0.9021 (m-80) cc_final: 0.8600 (m-10) REVERT: H 38 ARG cc_start: 0.7036 (ppp-140) cc_final: 0.6611 (ptm-80) REVERT: H 46 GLU cc_start: 0.7640 (pp20) cc_final: 0.7367 (pp20) REVERT: H 82 MET cc_start: 0.6629 (tmt) cc_final: 0.6291 (tmt) REVERT: H 99 TRP cc_start: 0.6782 (t60) cc_final: 0.6379 (t-100) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 1.2718 time to fit residues: 119.9435 Evaluate side-chains 78 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 134 optimal weight: 0.0030 chunk 197 optimal weight: 10.0000 chunk 297 optimal weight: 30.0000 chunk 274 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN C 856 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24827 Z= 0.140 Angle : 0.461 9.054 33791 Z= 0.232 Chirality : 0.043 0.350 4020 Planarity : 0.003 0.040 4294 Dihedral : 4.686 53.409 4452 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.68 % Allowed : 9.97 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.15), residues: 2951 helix: 2.83 (0.20), residues: 646 sheet: 0.25 (0.20), residues: 656 loop : -0.26 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 104 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE C 238 TYR 0.018 0.001 TYR H 94 ARG 0.005 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5902 Ramachandran restraints generated. 2951 Oldfield, 0 Emsley, 2951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7137 (mpp) cc_final: 0.6321 (tpt) REVERT: B 740 MET cc_start: 0.8777 (tpp) cc_final: 0.8185 (ttt) REVERT: B 990 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 1050 MET cc_start: 0.9123 (ptm) cc_final: 0.8722 (ptm) REVERT: B 1145 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7384 (tm) REVERT: C 421 TYR cc_start: 0.9014 (m-80) cc_final: 0.8593 (m-10) REVERT: C 455 LEU cc_start: 0.8480 (pt) cc_final: 0.8215 (pt) REVERT: C 740 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8411 (tmm) REVERT: H 38 ARG cc_start: 0.7106 (ppp-140) cc_final: 0.6635 (ptm-80) REVERT: H 46 GLU cc_start: 0.7623 (pp20) cc_final: 0.7288 (pp20) REVERT: H 82 MET cc_start: 0.6682 (tmt) cc_final: 0.6353 (tmt) REVERT: H 99 TRP cc_start: 0.6714 (t60) cc_final: 0.6353 (t60) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 1.2722 time to fit residues: 123.1044 Evaluate side-chains 78 residues out of total 2629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain H residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055318 restraints weight = 74533.025| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.33 r_work: 0.2962 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24827 Z= 0.184 Angle : 0.475 9.089 33791 Z= 0.239 Chirality : 0.044 0.347 4020 Planarity : 0.004 0.107 4294 Dihedral : 4.654 52.711 4452 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.57 % Allowed : 10.19 % Favored : 89.24 % 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: 0.79 (0.15), residues: 2951 helix: 2.81 (0.20), residues: 647 sheet: 0.27 (0.20), residues: 658 loop : -0.28 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 104 HIS 0.003 0.000 HIS H 35 PHE 0.031 0.001 PHE C 456 TYR 0.018 0.001 TYR H 94 ARG 0.007 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6792.62 seconds wall clock time: 123 minutes 42.49 seconds (7422.49 seconds total)