Starting phenix.real_space_refine on Thu May 22 17:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlz_27521/05_2025/8dlz_27521.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 100 5.16 5 C 14605 2.51 5 N 3756 2.21 5 O 4513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22974 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 840, 6549 Classifications: {'peptide': 840} Link IDs: {'PTRANS': 45, 'TRANS': 794} Chain breaks: 8 Chain: "B" Number of atoms: 6572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6572 Classifications: {'peptide': 843} Link IDs: {'PTRANS': 45, 'TRANS': 797} Chain breaks: 8 Chain: "C" Number of atoms: 8132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8132 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 14.83, per 1000 atoms: 0.65 Number of scatterers: 22974 At special positions: 0 Unit cell: (140, 146, 183, 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 100 16.00 O 4513 8.00 N 3756 7.00 C 14605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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=2.04 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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 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: 6.33 Conformation dependent library (CDL) restraints added in 3.1 seconds 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5322 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 36 sheets defined 25.4% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 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: 3.675A 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: 3.955A 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 1032 removed outlier: 4.040A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.542A 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: 3.965A 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: 3.582A 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 removed outlier: 3.510A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.909A 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: 3.972A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.844A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.532A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.636A 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 389 removed outlier: 4.075A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.581A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.308A 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: 3.882A 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: 3.652A 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: 3.948A 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: 3.552A 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: 4.330A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.550A pdb=" N ASP H 89 " --> pdb=" O ARG H 86 " (cutoff:3.500A) removed outlier: 4.042A 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: 6.409A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.885A 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: 3.504A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.019A 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: 11.330A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.900A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.503A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.692A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.932A 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: 5.182A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.050A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.817A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, 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: 3.834A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.730A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB4, 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: 5.994A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.133A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.569A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (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=AB7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.756A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.595A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.631A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC2, 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: 4.563A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.347A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC5, 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: 6.346A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.004A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.481A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.222A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.172A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.610A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD2, 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=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.279A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD5, 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: 3.863A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.300A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.201A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2415 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: 9.93 Time building geometry restraints manager: 7.30 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: 7019 1.34 - 1.46: 5741 1.46 - 1.58: 10580 1.58 - 1.71: 2 1.71 - 1.83: 130 Bond restraints: 23472 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.528 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1 NAG C1304 " pdb=" C2 NAG C1304 " ideal model delta sigma weight residual 1.532 1.591 -0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+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 6.26e+00 ... (remaining 23467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 30949 2.15 - 4.31: 902 4.31 - 6.46: 71 6.46 - 8.62: 18 8.62 - 10.77: 5 Bond angle restraints: 31945 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.66 -5.96 1.22e+00 6.72e-01 2.39e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.24 -5.54 1.22e+00 6.72e-01 2.06e+01 angle pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 112.00 105.76 6.24 1.40e+00 5.10e-01 1.99e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.93 -5.23 1.22e+00 6.72e-01 1.83e+01 angle pdb=" CB GLU C 465 " pdb=" CG GLU C 465 " pdb=" CD GLU C 465 " ideal model delta sigma weight residual 112.60 119.36 -6.76 1.70e+00 3.46e-01 1.58e+01 ... (remaining 31940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13563 17.88 - 35.77: 925 35.77 - 53.65: 162 53.65 - 71.53: 64 71.53 - 89.41: 26 Dihedral angle restraints: 14740 sinusoidal: 6487 harmonic: 8253 Sorted by residual: dihedral pdb=" CA ASN C 487 " pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 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 93.00 129.87 -36.87 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N GLU C 484 " pdb=" CA GLU C 484 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 14737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2953 0.063 - 0.126: 747 0.126 - 0.189: 101 0.189 - 0.252: 15 0.252 - 0.314: 3 Chirality restraints: 3819 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 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+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 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+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 2.02e+00 ... (remaining 3816 not shown) Planarity restraints: 4094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.044 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO H 14 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C MET C 902 " 0.040 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C VAL C 551 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.013 2.00e-02 2.50e+03 ... (remaining 4091 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6431 2.82 - 3.34: 19506 3.34 - 3.86: 39344 3.86 - 4.38: 45075 4.38 - 4.90: 77310 Nonbonded interactions: 187666 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.321 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.332 3.040 ... (remaining 187661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 330 or resid 531 through 1147 or resid 1301 thr \ ough 1306)) } 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: 5.500 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: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 55.830 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.140 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 0.122 23564 Z= 0.243 Angle : 0.859 15.231 32186 Z= 0.451 Chirality : 0.056 0.314 3819 Planarity : 0.006 0.064 4055 Dihedral : 13.173 89.414 9313 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.83 % 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: 2788 helix: 1.24 (0.19), residues: 603 sheet: 0.31 (0.19), residues: 670 loop : -0.82 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 886 HIS 0.005 0.001 HIS H 35 PHE 0.034 0.002 PHE A 275 TYR 0.033 0.002 TYR C1067 ARG 0.013 0.001 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 39) link_NAG-ASN : angle 3.65038 ( 117) link_BETA1-4 : bond 0.00648 ( 18) link_BETA1-4 : angle 1.22406 ( 54) hydrogen bonds : bond 0.12842 ( 870) hydrogen bonds : angle 7.00932 ( 2415) SS BOND : bond 0.00266 ( 35) SS BOND : angle 1.36632 ( 70) covalent geometry : bond 0.00515 (23472) covalent geometry : angle 0.82946 (31945) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.5413 (p90) cc_final: 0.5043 (p90) REVERT: A 541 PHE cc_start: 0.7652 (p90) cc_final: 0.7369 (p90) REVERT: A 985 ASP cc_start: 0.7780 (m-30) cc_final: 0.7453 (m-30) REVERT: A 1029 MET cc_start: 0.9340 (tpp) cc_final: 0.9062 (tpp) REVERT: B 129 LYS cc_start: 0.6367 (mtmt) cc_final: 0.6126 (tppp) REVERT: B 153 MET cc_start: 0.5560 (mpp) cc_final: 0.4993 (pp-130) REVERT: B 201 PHE cc_start: 0.7093 (t80) cc_final: 0.6729 (t80) REVERT: B 207 HIS cc_start: 0.6566 (t-170) cc_final: 0.5747 (t-170) REVERT: B 327 VAL cc_start: 0.8520 (t) cc_final: 0.8246 (m) REVERT: B 858 LEU cc_start: 0.8449 (mt) cc_final: 0.7859 (pt) REVERT: B 900 MET cc_start: 0.8616 (mtp) cc_final: 0.8401 (ttm) REVERT: C 30 ASN cc_start: 0.7538 (t0) cc_final: 0.7211 (t0) REVERT: C 54 LEU cc_start: 0.8734 (mm) cc_final: 0.8226 (mt) REVERT: C 104 TRP cc_start: 0.7491 (m-90) cc_final: 0.7280 (m-90) REVERT: C 133 PHE cc_start: 0.6047 (m-80) cc_final: 0.5396 (m-80) REVERT: C 207 HIS cc_start: 0.7147 (m-70) cc_final: 0.6541 (t-90) REVERT: C 334 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7049 (p0) REVERT: C 378 LYS cc_start: 0.8778 (mttm) cc_final: 0.8568 (mttp) REVERT: C 396 TYR cc_start: 0.6994 (m-80) cc_final: 0.5137 (m-10) REVERT: C 403 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7357 (ptt-90) REVERT: C 424 LYS cc_start: 0.8762 (tptt) cc_final: 0.8532 (tptt) REVERT: C 433 VAL cc_start: 0.8709 (t) cc_final: 0.8390 (m) REVERT: C 532 ASN cc_start: 0.8530 (t0) cc_final: 0.8250 (p0) REVERT: C 987 PRO cc_start: 0.7958 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: C 988 GLU cc_start: 0.8083 (mp0) cc_final: 0.7657 (mp0) REVERT: C 1002 GLN cc_start: 0.8456 (tt0) cc_final: 0.8211 (tt0) outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 1.2554 time to fit residues: 431.4909 Evaluate side-chains 141 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 2.655 ------------------------------------------------------------------------------- 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: 283 random chunks: chunk 238 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 955 ASN A1011 GLN B 762 GLN B 779 GLN B 901 GLN C 121 ASN C 580 GLN C 957 GLN C1002 GLN H 35 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078820 restraints weight = 46435.360| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.84 r_work: 0.3139 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23564 Z= 0.129 Angle : 0.600 11.604 32186 Z= 0.295 Chirality : 0.045 0.256 3819 Planarity : 0.004 0.050 4055 Dihedral : 6.603 59.970 4227 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 6.87 % Favored : 91.80 % 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: 0.39 (0.15), residues: 2788 helix: 2.16 (0.21), residues: 618 sheet: 0.51 (0.20), residues: 606 loop : -0.62 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.005 0.001 HIS B 207 PHE 0.021 0.001 PHE A 133 TYR 0.023 0.001 TYR B 28 ARG 0.006 0.000 ARG B 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 39) link_NAG-ASN : angle 3.33038 ( 117) link_BETA1-4 : bond 0.00301 ( 18) link_BETA1-4 : angle 1.06229 ( 54) hydrogen bonds : bond 0.04274 ( 870) hydrogen bonds : angle 5.76761 ( 2415) SS BOND : bond 0.00426 ( 35) SS BOND : angle 1.54074 ( 70) covalent geometry : bond 0.00287 (23472) covalent geometry : angle 0.56166 (31945) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8725 (tt0) cc_final: 0.8042 (tm-30) REVERT: A 780 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8756 (mm-30) REVERT: A 979 ASP cc_start: 0.7729 (m-30) cc_final: 0.7372 (t0) REVERT: A 1029 MET cc_start: 0.9609 (tpp) cc_final: 0.9378 (tpp) REVERT: B 102 ARG cc_start: 0.6806 (mmp-170) cc_final: 0.6466 (mmp-170) REVERT: B 118 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6539 (mp) REVERT: B 129 LYS cc_start: 0.6339 (mtmt) cc_final: 0.6008 (tppp) REVERT: B 153 MET cc_start: 0.5544 (mpp) cc_final: 0.4946 (pp-130) REVERT: B 201 PHE cc_start: 0.7280 (t80) cc_final: 0.6758 (t80) REVERT: B 327 VAL cc_start: 0.8076 (t) cc_final: 0.7699 (m) REVERT: B 858 LEU cc_start: 0.8699 (mt) cc_final: 0.7837 (pt) REVERT: B 900 MET cc_start: 0.9128 (mtp) cc_final: 0.8861 (ttm) REVERT: B 934 ILE cc_start: 0.8363 (mm) cc_final: 0.8157 (mp) REVERT: B 957 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8317 (pp30) REVERT: C 30 ASN cc_start: 0.7758 (t0) cc_final: 0.7286 (t0) REVERT: C 64 TRP cc_start: 0.7637 (t60) cc_final: 0.7364 (t60) REVERT: C 207 HIS cc_start: 0.7404 (m-70) cc_final: 0.6516 (t-90) REVERT: C 334 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.7008 (p0) REVERT: C 420 ASP cc_start: 0.8276 (t0) cc_final: 0.8062 (t0) REVERT: C 424 LYS cc_start: 0.8565 (tptt) cc_final: 0.8268 (tptt) REVERT: C 433 VAL cc_start: 0.8364 (t) cc_final: 0.8092 (m) REVERT: C 532 ASN cc_start: 0.8890 (t0) cc_final: 0.8227 (p0) REVERT: C 990 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 1002 GLN cc_start: 0.8967 (tt0) cc_final: 0.8699 (tt0) outliers start: 33 outliers final: 9 residues processed: 186 average time/residue: 1.2032 time to fit residues: 261.6764 Evaluate side-chains 144 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 253 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 195 optimal weight: 0.0770 chunk 110 optimal weight: 0.0370 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B1010 GLN C 196 ASN C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.128203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079136 restraints weight = 46243.981| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.84 r_work: 0.3146 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 23564 Z= 0.106 Angle : 0.553 10.437 32186 Z= 0.271 Chirality : 0.044 0.260 3819 Planarity : 0.004 0.052 4055 Dihedral : 5.864 58.946 4227 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.37 % Allowed : 7.71 % Favored : 90.92 % 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: 0.57 (0.15), residues: 2788 helix: 2.58 (0.21), residues: 616 sheet: 0.33 (0.21), residues: 588 loop : -0.49 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.006 0.001 HIS H 35 PHE 0.023 0.001 PHE C 168 TYR 0.023 0.001 TYR B 28 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 39) link_NAG-ASN : angle 3.04720 ( 117) link_BETA1-4 : bond 0.00359 ( 18) link_BETA1-4 : angle 1.02779 ( 54) hydrogen bonds : bond 0.03926 ( 870) hydrogen bonds : angle 5.41704 ( 2415) SS BOND : bond 0.00279 ( 35) SS BOND : angle 1.26609 ( 70) covalent geometry : bond 0.00233 (23472) covalent geometry : angle 0.51876 (31945) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7272 (m-80) cc_final: 0.6804 (m-80) REVERT: A 298 GLU cc_start: 0.8724 (tt0) cc_final: 0.8027 (tm-30) REVERT: A 780 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8722 (mm-30) REVERT: A 979 ASP cc_start: 0.7623 (m-30) cc_final: 0.7300 (t0) REVERT: A 1029 MET cc_start: 0.9575 (tpp) cc_final: 0.9341 (tpp) REVERT: B 118 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6479 (mp) REVERT: B 129 LYS cc_start: 0.6163 (mtmt) cc_final: 0.5834 (ttmt) REVERT: B 153 MET cc_start: 0.5293 (mpp) cc_final: 0.4783 (pp-130) REVERT: B 190 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7452 (ttp-170) REVERT: B 201 PHE cc_start: 0.7316 (t80) cc_final: 0.6893 (t80) REVERT: B 327 VAL cc_start: 0.7996 (t) cc_final: 0.7581 (m) REVERT: B 554 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7987 (mm-30) REVERT: B 858 LEU cc_start: 0.8757 (mt) cc_final: 0.7907 (pt) REVERT: B 900 MET cc_start: 0.9108 (mtp) cc_final: 0.8876 (ttm) REVERT: B 957 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8277 (pp30) REVERT: B 964 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8694 (mmmm) REVERT: C 30 ASN cc_start: 0.7690 (t0) cc_final: 0.7217 (t0) REVERT: C 64 TRP cc_start: 0.7573 (t60) cc_final: 0.7331 (t60) REVERT: C 334 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.6970 (p0) REVERT: C 408 ARG cc_start: 0.8411 (ppt170) cc_final: 0.8016 (ptm-80) REVERT: C 433 VAL cc_start: 0.8251 (t) cc_final: 0.7988 (m) REVERT: C 532 ASN cc_start: 0.8911 (t0) cc_final: 0.8240 (p0) REVERT: C 981 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8533 (mm) REVERT: C 990 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7440 (tm-30) REVERT: C 1002 GLN cc_start: 0.8920 (tt0) cc_final: 0.8699 (tt0) REVERT: H 60 ASN cc_start: 0.4810 (t0) cc_final: 0.4577 (t0) outliers start: 34 outliers final: 7 residues processed: 179 average time/residue: 1.1024 time to fit residues: 237.8246 Evaluate side-chains 143 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 185 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B1010 GLN C 49 HIS C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075361 restraints weight = 46423.471| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.81 r_work: 0.3080 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 23564 Z= 0.185 Angle : 0.587 11.125 32186 Z= 0.288 Chirality : 0.045 0.279 3819 Planarity : 0.004 0.047 4055 Dihedral : 5.569 58.059 4227 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.73 % Allowed : 8.52 % Favored : 89.75 % 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: 0.44 (0.15), residues: 2788 helix: 2.50 (0.21), residues: 619 sheet: 0.03 (0.20), residues: 607 loop : -0.49 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE C 168 TYR 0.022 0.002 TYR B 28 ARG 0.005 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 39) link_NAG-ASN : angle 3.04681 ( 117) link_BETA1-4 : bond 0.00223 ( 18) link_BETA1-4 : angle 1.15280 ( 54) hydrogen bonds : bond 0.04298 ( 870) hydrogen bonds : angle 5.39398 ( 2415) SS BOND : bond 0.00260 ( 35) SS BOND : angle 1.56994 ( 70) covalent geometry : bond 0.00425 (23472) covalent geometry : angle 0.55248 (31945) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2999 (pp-130) cc_final: 0.2787 (pp-130) REVERT: A 200 TYR cc_start: 0.7457 (m-80) cc_final: 0.6908 (m-80) REVERT: A 298 GLU cc_start: 0.8769 (tt0) cc_final: 0.8086 (tm-30) REVERT: A 979 ASP cc_start: 0.7764 (m-30) cc_final: 0.7419 (t0) REVERT: B 102 ARG cc_start: 0.6518 (mmp-170) cc_final: 0.6002 (mmp-170) REVERT: B 118 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6458 (mp) REVERT: B 129 LYS cc_start: 0.6177 (mtmt) cc_final: 0.5931 (ttmt) REVERT: B 153 MET cc_start: 0.5318 (mpp) cc_final: 0.4726 (pp-130) REVERT: B 201 PHE cc_start: 0.7428 (t80) cc_final: 0.7027 (t80) REVERT: B 239 GLN cc_start: 0.7268 (tt0) cc_final: 0.6302 (tm-30) REVERT: B 327 VAL cc_start: 0.8077 (t) cc_final: 0.7691 (m) REVERT: B 554 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7920 (mm-30) REVERT: B 740 MET cc_start: 0.8832 (ttt) cc_final: 0.8520 (ttm) REVERT: B 858 LEU cc_start: 0.8964 (mt) cc_final: 0.8012 (pt) REVERT: B 957 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8230 (pp30) REVERT: B 964 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8706 (mmmm) REVERT: B 990 GLU cc_start: 0.8293 (tt0) cc_final: 0.8018 (tm-30) REVERT: C 30 ASN cc_start: 0.7666 (t0) cc_final: 0.7157 (t0) REVERT: C 64 TRP cc_start: 0.7645 (t60) cc_final: 0.7341 (t60) REVERT: C 218 GLN cc_start: 0.8501 (tt0) cc_final: 0.8240 (tp40) REVERT: C 227 VAL cc_start: 0.8830 (t) cc_final: 0.8609 (m) REVERT: C 334 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6878 (p0) REVERT: C 433 VAL cc_start: 0.8264 (t) cc_final: 0.7989 (m) REVERT: C 455 LEU cc_start: 0.8381 (tp) cc_final: 0.8032 (pp) REVERT: C 532 ASN cc_start: 0.8936 (t0) cc_final: 0.8227 (p0) REVERT: C 990 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 1002 GLN cc_start: 0.8933 (tt0) cc_final: 0.8695 (tt0) REVERT: H 32 TYR cc_start: 0.5212 (OUTLIER) cc_final: 0.4976 (t80) REVERT: H 60 ASN cc_start: 0.4799 (t0) cc_final: 0.4547 (t0) outliers start: 43 outliers final: 11 residues processed: 179 average time/residue: 1.0767 time to fit residues: 230.0764 Evaluate side-chains 149 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL 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 C residue 569 ILE Chi-restraints excluded: chain H residue 32 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 194 optimal weight: 0.0060 chunk 217 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 755 GLN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.125764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.076007 restraints weight = 46378.451| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.83 r_work: 0.3074 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23564 Z= 0.133 Angle : 0.552 10.410 32186 Z= 0.268 Chirality : 0.044 0.270 3819 Planarity : 0.003 0.035 4055 Dihedral : 5.224 53.522 4227 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.57 % Allowed : 8.88 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2788 helix: 2.60 (0.21), residues: 624 sheet: 0.15 (0.20), residues: 594 loop : -0.48 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS H 35 PHE 0.023 0.001 PHE C 168 TYR 0.020 0.001 TYR B 28 ARG 0.004 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 39) link_NAG-ASN : angle 2.93913 ( 117) link_BETA1-4 : bond 0.00331 ( 18) link_BETA1-4 : angle 1.03761 ( 54) hydrogen bonds : bond 0.03974 ( 870) hydrogen bonds : angle 5.24458 ( 2415) SS BOND : bond 0.00312 ( 35) SS BOND : angle 1.07660 ( 70) covalent geometry : bond 0.00303 (23472) covalent geometry : angle 0.52075 (31945) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6617 (tt) REVERT: A 134 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6897 (mm110) REVERT: A 160 TYR cc_start: 0.5644 (p90) cc_final: 0.5274 (p90) REVERT: A 298 GLU cc_start: 0.8782 (tt0) cc_final: 0.8041 (tm-30) REVERT: A 856 ASN cc_start: 0.6727 (OUTLIER) cc_final: 0.6425 (m110) REVERT: A 964 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8726 (mtpp) REVERT: A 979 ASP cc_start: 0.7802 (m-30) cc_final: 0.7483 (t0) REVERT: B 118 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 129 LYS cc_start: 0.6202 (mtmt) cc_final: 0.5796 (ttmt) REVERT: B 153 MET cc_start: 0.5326 (mpp) cc_final: 0.4670 (pp-130) REVERT: B 201 PHE cc_start: 0.7544 (t80) cc_final: 0.7171 (t80) REVERT: B 207 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: B 239 GLN cc_start: 0.7239 (tt0) cc_final: 0.6241 (tm-30) REVERT: B 554 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7906 (mm-30) REVERT: B 740 MET cc_start: 0.8723 (ttt) cc_final: 0.8370 (ttm) REVERT: B 858 LEU cc_start: 0.8960 (mt) cc_final: 0.8060 (pt) REVERT: B 934 ILE cc_start: 0.8359 (mm) cc_final: 0.8146 (mp) REVERT: B 957 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8239 (pp30) REVERT: B 964 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8742 (mmmm) REVERT: C 30 ASN cc_start: 0.7622 (t0) cc_final: 0.7135 (t0) REVERT: C 64 TRP cc_start: 0.7637 (t60) cc_final: 0.7327 (t60) REVERT: C 218 GLN cc_start: 0.8455 (tt0) cc_final: 0.8201 (tp40) REVERT: C 324 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: C 334 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6878 (p0) REVERT: C 408 ARG cc_start: 0.8320 (ppt170) cc_final: 0.7912 (ptm-80) REVERT: C 455 LEU cc_start: 0.8386 (tp) cc_final: 0.8015 (pp) REVERT: C 532 ASN cc_start: 0.8946 (t0) cc_final: 0.8264 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8457 (tt0) cc_final: 0.8214 (tt0) REVERT: C 990 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 1002 GLN cc_start: 0.8955 (tt0) cc_final: 0.8710 (tt0) REVERT: C 1010 GLN cc_start: 0.8955 (tp40) cc_final: 0.8737 (mp10) REVERT: H 60 ASN cc_start: 0.4723 (t0) cc_final: 0.4509 (t0) outliers start: 39 outliers final: 10 residues processed: 177 average time/residue: 1.1328 time to fit residues: 237.0614 Evaluate side-chains 154 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 145 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 209 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 chunk 258 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 167 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 824 ASN B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.125174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075423 restraints weight = 46195.964| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.81 r_work: 0.3061 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23564 Z= 0.152 Angle : 0.563 10.456 32186 Z= 0.274 Chirality : 0.044 0.275 3819 Planarity : 0.003 0.036 4055 Dihedral : 5.018 52.084 4227 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.45 % Allowed : 10.00 % Favored : 88.55 % 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: 0.52 (0.15), residues: 2788 helix: 2.65 (0.20), residues: 624 sheet: 0.08 (0.20), residues: 613 loop : -0.50 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.004 0.001 HIS H 35 PHE 0.024 0.001 PHE C 168 TYR 0.023 0.001 TYR H 32 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 39) link_NAG-ASN : angle 2.90798 ( 117) link_BETA1-4 : bond 0.00242 ( 18) link_BETA1-4 : angle 1.06879 ( 54) hydrogen bonds : bond 0.04040 ( 870) hydrogen bonds : angle 5.18559 ( 2415) SS BOND : bond 0.00171 ( 35) SS BOND : angle 1.17685 ( 70) covalent geometry : bond 0.00348 (23472) covalent geometry : angle 0.53270 (31945) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7708 (mm) REVERT: A 134 GLN cc_start: 0.7082 (mm110) cc_final: 0.6845 (mm110) REVERT: A 160 TYR cc_start: 0.5600 (p90) cc_final: 0.5386 (p90) REVERT: A 298 GLU cc_start: 0.8766 (tt0) cc_final: 0.8084 (tm-30) REVERT: A 856 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6538 (m110) REVERT: A 979 ASP cc_start: 0.7820 (m-30) cc_final: 0.7475 (t0) REVERT: B 102 ARG cc_start: 0.6458 (mmp-170) cc_final: 0.6152 (mmp-170) REVERT: B 118 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6449 (mp) REVERT: B 129 LYS cc_start: 0.6180 (mtmt) cc_final: 0.5847 (ttmt) REVERT: B 153 MET cc_start: 0.5265 (mpp) cc_final: 0.4470 (pp-130) REVERT: B 201 PHE cc_start: 0.7550 (t80) cc_final: 0.7168 (t80) REVERT: B 207 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: B 239 GLN cc_start: 0.7233 (tt0) cc_final: 0.6791 (tt0) REVERT: B 554 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7891 (mm-30) REVERT: B 934 ILE cc_start: 0.8406 (mm) cc_final: 0.8204 (mp) REVERT: B 957 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8249 (pp30) REVERT: B 964 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8751 (mmmm) REVERT: B 990 GLU cc_start: 0.8312 (tt0) cc_final: 0.8021 (tm-30) REVERT: C 30 ASN cc_start: 0.7608 (t0) cc_final: 0.7059 (t0) REVERT: C 64 TRP cc_start: 0.7657 (t60) cc_final: 0.7334 (t60) REVERT: C 187 LYS cc_start: 0.6653 (mmtp) cc_final: 0.6276 (ptpt) REVERT: C 218 GLN cc_start: 0.8466 (tt0) cc_final: 0.8202 (tp40) REVERT: C 324 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: C 334 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6865 (p0) REVERT: C 455 LEU cc_start: 0.8387 (tp) cc_final: 0.8010 (pp) REVERT: C 532 ASN cc_start: 0.8901 (t0) cc_final: 0.8295 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8464 (tt0) cc_final: 0.8221 (tt0) REVERT: C 957 GLN cc_start: 0.8681 (tt0) cc_final: 0.8297 (tm-30) REVERT: C 990 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 1002 GLN cc_start: 0.8932 (tt0) cc_final: 0.8727 (tt0) REVERT: C 1010 GLN cc_start: 0.8952 (tp40) cc_final: 0.8729 (mp10) REVERT: H 32 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4748 (t80) outliers start: 36 outliers final: 11 residues processed: 171 average time/residue: 1.1822 time to fit residues: 238.7069 Evaluate side-chains 154 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 166 optimal weight: 0.9990 chunk 135 optimal weight: 0.0020 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 189 optimal weight: 9.9990 chunk 169 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 overall best weight: 0.5850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.076469 restraints weight = 46244.552| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.81 r_work: 0.3102 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23564 Z= 0.106 Angle : 0.539 10.480 32186 Z= 0.262 Chirality : 0.043 0.267 3819 Planarity : 0.003 0.036 4055 Dihedral : 4.794 52.633 4227 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.04 % Allowed : 10.73 % Favored : 88.23 % 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: 0.65 (0.16), residues: 2788 helix: 2.79 (0.21), residues: 618 sheet: 0.26 (0.20), residues: 626 loop : -0.47 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.004 0.000 HIS H 35 PHE 0.030 0.001 PHE B 194 TYR 0.022 0.001 TYR H 32 ARG 0.004 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 39) link_NAG-ASN : angle 2.79664 ( 117) link_BETA1-4 : bond 0.00332 ( 18) link_BETA1-4 : angle 0.99500 ( 54) hydrogen bonds : bond 0.03761 ( 870) hydrogen bonds : angle 5.05295 ( 2415) SS BOND : bond 0.00128 ( 35) SS BOND : angle 0.91439 ( 70) covalent geometry : bond 0.00236 (23472) covalent geometry : angle 0.51067 (31945) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7658 (mm) REVERT: A 160 TYR cc_start: 0.5743 (p90) cc_final: 0.5510 (p90) REVERT: A 298 GLU cc_start: 0.8763 (tt0) cc_final: 0.8083 (tm-30) REVERT: A 856 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6485 (m110) REVERT: A 979 ASP cc_start: 0.7759 (m-30) cc_final: 0.7432 (t0) REVERT: B 118 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6442 (mp) REVERT: B 129 LYS cc_start: 0.6191 (mtmt) cc_final: 0.5857 (ttmt) REVERT: B 153 MET cc_start: 0.5348 (mpp) cc_final: 0.4514 (pp-130) REVERT: B 201 PHE cc_start: 0.7548 (t80) cc_final: 0.7204 (t80) REVERT: B 239 GLN cc_start: 0.7190 (tt0) cc_final: 0.6255 (tm-30) REVERT: B 554 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7899 (mm-30) REVERT: B 740 MET cc_start: 0.8730 (ttt) cc_final: 0.8521 (ttp) REVERT: B 934 ILE cc_start: 0.8316 (mm) cc_final: 0.8107 (mp) REVERT: B 957 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8230 (pp30) REVERT: B 964 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8776 (mmmm) REVERT: C 30 ASN cc_start: 0.7586 (t0) cc_final: 0.7050 (t0) REVERT: C 64 TRP cc_start: 0.7671 (t60) cc_final: 0.7361 (t60) REVERT: C 113 LYS cc_start: 0.8270 (mttp) cc_final: 0.8060 (tppt) REVERT: C 187 LYS cc_start: 0.6656 (mmtp) cc_final: 0.6266 (ptpt) REVERT: C 218 GLN cc_start: 0.8445 (tt0) cc_final: 0.8195 (tp40) REVERT: C 324 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: C 334 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6809 (p0) REVERT: C 455 LEU cc_start: 0.8392 (tp) cc_final: 0.7994 (pp) REVERT: C 532 ASN cc_start: 0.9019 (t0) cc_final: 0.8303 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8442 (tt0) cc_final: 0.8194 (tt0) REVERT: C 957 GLN cc_start: 0.8674 (tt0) cc_final: 0.8295 (tm-30) REVERT: C 990 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 1002 GLN cc_start: 0.8924 (tt0) cc_final: 0.8700 (tt0) REVERT: C 1010 GLN cc_start: 0.8937 (tp40) cc_final: 0.8729 (mp10) REVERT: H 32 TYR cc_start: 0.4567 (OUTLIER) cc_final: 0.4107 (t80) outliers start: 26 outliers final: 11 residues processed: 159 average time/residue: 1.1355 time to fit residues: 213.2193 Evaluate side-chains 155 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 118 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.125707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076289 restraints weight = 46176.271| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.83 r_work: 0.3072 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23564 Z= 0.117 Angle : 0.535 10.523 32186 Z= 0.260 Chirality : 0.043 0.271 3819 Planarity : 0.003 0.037 4055 Dihedral : 4.600 52.613 4227 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.33 % Allowed : 10.49 % Favored : 88.19 % 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: 0.68 (0.16), residues: 2788 helix: 2.75 (0.21), residues: 624 sheet: 0.28 (0.20), residues: 630 loop : -0.44 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.001 PHE B 194 TYR 0.022 0.001 TYR B 170 ARG 0.006 0.000 ARG B 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 39) link_NAG-ASN : angle 2.75054 ( 117) link_BETA1-4 : bond 0.00305 ( 18) link_BETA1-4 : angle 1.01550 ( 54) hydrogen bonds : bond 0.03730 ( 870) hydrogen bonds : angle 4.97260 ( 2415) SS BOND : bond 0.00128 ( 35) SS BOND : angle 0.86097 ( 70) covalent geometry : bond 0.00264 (23472) covalent geometry : angle 0.50699 (31945) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7656 (mm) REVERT: A 134 GLN cc_start: 0.7124 (mm110) cc_final: 0.6838 (mm110) REVERT: A 160 TYR cc_start: 0.5835 (p90) cc_final: 0.5605 (p90) REVERT: A 200 TYR cc_start: 0.7647 (m-80) cc_final: 0.7405 (t80) REVERT: A 298 GLU cc_start: 0.8771 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 856 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6474 (m110) REVERT: A 964 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8746 (mtpp) REVERT: A 979 ASP cc_start: 0.7791 (m-30) cc_final: 0.7429 (t0) REVERT: B 118 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6389 (mp) REVERT: B 129 LYS cc_start: 0.6174 (mtmt) cc_final: 0.5785 (ttmt) REVERT: B 153 MET cc_start: 0.5245 (mpp) cc_final: 0.4434 (pp-130) REVERT: B 190 ARG cc_start: 0.7562 (ttm170) cc_final: 0.7208 (ttm170) REVERT: B 201 PHE cc_start: 0.7543 (t80) cc_final: 0.7066 (t80) REVERT: B 239 GLN cc_start: 0.7200 (tt0) cc_final: 0.6252 (tm-30) REVERT: B 554 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7904 (mm-30) REVERT: B 934 ILE cc_start: 0.8319 (mm) cc_final: 0.8105 (mp) REVERT: B 957 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8233 (pp30) REVERT: B 964 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8762 (mmmm) REVERT: C 30 ASN cc_start: 0.7626 (t0) cc_final: 0.7070 (t0) REVERT: C 187 LYS cc_start: 0.6694 (mmtp) cc_final: 0.6334 (ptpt) REVERT: C 218 GLN cc_start: 0.8454 (tt0) cc_final: 0.8198 (tp40) REVERT: C 324 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: C 455 LEU cc_start: 0.8373 (tp) cc_final: 0.7977 (pp) REVERT: C 532 ASN cc_start: 0.8971 (t0) cc_final: 0.8274 (OUTLIER) REVERT: C 773 GLU cc_start: 0.8460 (tt0) cc_final: 0.8208 (tt0) REVERT: C 957 GLN cc_start: 0.8669 (tt0) cc_final: 0.8292 (tm-30) REVERT: C 990 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7538 (tm-30) REVERT: C 1002 GLN cc_start: 0.8924 (tt0) cc_final: 0.8704 (tt0) REVERT: C 1010 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (mp10) REVERT: H 32 TYR cc_start: 0.4685 (OUTLIER) cc_final: 0.4431 (t80) outliers start: 33 outliers final: 14 residues processed: 171 average time/residue: 1.1181 time to fit residues: 225.9898 Evaluate side-chains 159 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 20 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 55 optimal weight: 0.0980 chunk 160 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B1010 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.125419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075891 restraints weight = 46276.043| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.81 r_work: 0.3071 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23564 Z= 0.128 Angle : 0.545 10.703 32186 Z= 0.266 Chirality : 0.044 0.271 3819 Planarity : 0.003 0.038 4055 Dihedral : 4.548 52.337 4225 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.21 % Allowed : 10.89 % Favored : 87.91 % 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: 0.68 (0.16), residues: 2788 helix: 2.74 (0.21), residues: 625 sheet: 0.25 (0.21), residues: 620 loop : -0.41 (0.15), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.004 0.001 HIS H 35 PHE 0.026 0.001 PHE C 168 TYR 0.017 0.001 TYR A 28 ARG 0.006 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 39) link_NAG-ASN : angle 2.71525 ( 117) link_BETA1-4 : bond 0.00297 ( 18) link_BETA1-4 : angle 1.01198 ( 54) hydrogen bonds : bond 0.03780 ( 870) hydrogen bonds : angle 4.99144 ( 2415) SS BOND : bond 0.00150 ( 35) SS BOND : angle 0.86590 ( 70) covalent geometry : bond 0.00293 (23472) covalent geometry : angle 0.51855 (31945) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7696 (mm) REVERT: A 134 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6668 (mm110) REVERT: A 160 TYR cc_start: 0.5775 (p90) cc_final: 0.5531 (p90) REVERT: A 298 GLU cc_start: 0.8776 (tt0) cc_final: 0.8140 (tm-30) REVERT: A 856 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6426 (m110) REVERT: A 979 ASP cc_start: 0.7823 (m-30) cc_final: 0.7458 (OUTLIER) REVERT: B 88 ASP cc_start: 0.7760 (m-30) cc_final: 0.6803 (p0) REVERT: B 102 ARG cc_start: 0.6400 (mmp-170) cc_final: 0.5916 (mmp-170) REVERT: B 118 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6428 (mp) REVERT: B 129 LYS cc_start: 0.6197 (mtmt) cc_final: 0.5835 (tttt) REVERT: B 153 MET cc_start: 0.5198 (mpp) cc_final: 0.4304 (pp-130) REVERT: B 201 PHE cc_start: 0.7559 (t80) cc_final: 0.7075 (t80) REVERT: B 239 GLN cc_start: 0.7168 (tt0) cc_final: 0.6231 (tm-30) REVERT: B 269 TYR cc_start: 0.7980 (m-80) cc_final: 0.7769 (m-80) REVERT: B 554 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7926 (mm-30) REVERT: B 934 ILE cc_start: 0.8351 (mm) cc_final: 0.8131 (mp) REVERT: B 957 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8224 (pp30) REVERT: B 964 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8729 (mmmm) REVERT: C 30 ASN cc_start: 0.7744 (t0) cc_final: 0.7112 (t0) REVERT: C 64 TRP cc_start: 0.7477 (t60) cc_final: 0.7233 (t60) REVERT: C 187 LYS cc_start: 0.6740 (mmtp) cc_final: 0.6422 (ptpt) REVERT: C 218 GLN cc_start: 0.8465 (tt0) cc_final: 0.8219 (tp40) REVERT: C 324 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8150 (pm20) REVERT: C 334 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6850 (p0) REVERT: C 455 LEU cc_start: 0.8375 (tp) cc_final: 0.7993 (pp) REVERT: C 532 ASN cc_start: 0.8971 (t0) cc_final: 0.8449 (m110) REVERT: C 773 GLU cc_start: 0.8469 (tt0) cc_final: 0.8217 (tt0) REVERT: C 957 GLN cc_start: 0.8667 (tt0) cc_final: 0.8291 (tm-30) REVERT: C 985 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7676 (p0) REVERT: C 990 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 1002 GLN cc_start: 0.8928 (tt0) cc_final: 0.8710 (tt0) REVERT: C 1010 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8728 (mp10) REVERT: H 34 MET cc_start: 0.5977 (pmm) cc_final: 0.2859 (mpp) outliers start: 30 outliers final: 14 residues processed: 160 average time/residue: 1.1329 time to fit residues: 214.2057 Evaluate side-chains 158 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 269 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 207 HIS B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.124681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075011 restraints weight = 46216.291| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.82 r_work: 0.3072 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 23564 Z= 0.161 Angle : 0.575 12.682 32186 Z= 0.283 Chirality : 0.045 0.274 3819 Planarity : 0.004 0.056 4055 Dihedral : 4.646 52.061 4225 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.00 % Allowed : 11.13 % Favored : 87.87 % 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: 0.59 (0.16), residues: 2788 helix: 2.67 (0.20), residues: 631 sheet: 0.12 (0.21), residues: 596 loop : -0.44 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.001 PHE C 168 TYR 0.034 0.001 TYR H 32 ARG 0.009 0.000 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 39) link_NAG-ASN : angle 2.73958 ( 117) link_BETA1-4 : bond 0.00276 ( 18) link_BETA1-4 : angle 1.05699 ( 54) hydrogen bonds : bond 0.04028 ( 870) hydrogen bonds : angle 5.09848 ( 2415) SS BOND : bond 0.00187 ( 35) SS BOND : angle 1.63860 ( 70) covalent geometry : bond 0.00377 (23472) covalent geometry : angle 0.54548 (31945) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.6962 (OUTLIER) cc_final: 0.6695 (mm110) REVERT: A 160 TYR cc_start: 0.5800 (p90) cc_final: 0.5564 (p90) REVERT: A 298 GLU cc_start: 0.8747 (tt0) cc_final: 0.8101 (tm-30) REVERT: A 856 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6494 (m110) REVERT: A 979 ASP cc_start: 0.7831 (m-30) cc_final: 0.7440 (t0) REVERT: B 118 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6286 (mp) REVERT: B 129 LYS cc_start: 0.6214 (mtmt) cc_final: 0.5806 (ttmt) REVERT: B 153 MET cc_start: 0.5199 (mpp) cc_final: 0.4259 (pp-130) REVERT: B 201 PHE cc_start: 0.7571 (t80) cc_final: 0.7079 (t80) REVERT: B 239 GLN cc_start: 0.7092 (tt0) cc_final: 0.6700 (tt0) REVERT: B 554 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7901 (mm-30) REVERT: B 934 ILE cc_start: 0.8366 (mm) cc_final: 0.8141 (mp) REVERT: B 964 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8702 (mmmm) REVERT: B 990 GLU cc_start: 0.8269 (tt0) cc_final: 0.7990 (tm-30) REVERT: C 64 TRP cc_start: 0.7430 (t60) cc_final: 0.7160 (t60) REVERT: C 187 LYS cc_start: 0.6895 (mmtp) cc_final: 0.6523 (ptpt) REVERT: C 218 GLN cc_start: 0.8426 (tt0) cc_final: 0.8211 (tp40) REVERT: C 324 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: C 334 ASN cc_start: 0.7358 (OUTLIER) cc_final: 0.6856 (p0) REVERT: C 421 TYR cc_start: 0.8040 (m-80) cc_final: 0.7809 (m-80) REVERT: C 455 LEU cc_start: 0.8403 (tp) cc_final: 0.8022 (pp) REVERT: C 532 ASN cc_start: 0.9009 (t0) cc_final: 0.8481 (m110) REVERT: C 773 GLU cc_start: 0.8400 (tt0) cc_final: 0.8041 (tt0) REVERT: C 869 MET cc_start: 0.9242 (mtt) cc_final: 0.8891 (mtt) REVERT: C 957 GLN cc_start: 0.8629 (tt0) cc_final: 0.8240 (tm-30) REVERT: C 985 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7677 (p0) REVERT: C 990 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 1002 GLN cc_start: 0.8906 (tt0) cc_final: 0.8672 (tt0) REVERT: C 1010 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8701 (mp10) outliers start: 25 outliers final: 13 residues processed: 159 average time/residue: 1.1238 time to fit residues: 211.0939 Evaluate side-chains 157 residues out of total 2489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain H residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 144 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 182 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 207 HIS B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.125219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075766 restraints weight = 46026.319| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.83 r_work: 0.3085 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23564 Z= 0.126 Angle : 0.550 11.336 32186 Z= 0.270 Chirality : 0.044 0.269 3819 Planarity : 0.003 0.049 4055 Dihedral : 4.582 52.377 4225 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.12 % Allowed : 11.17 % Favored : 87.71 % 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 (0.16), residues: 2788 helix: 2.67 (0.21), residues: 626 sheet: 0.25 (0.20), residues: 648 loop : -0.40 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 353 HIS 0.004 0.001 HIS H 35 PHE 0.027 0.001 PHE C 168 TYR 0.023 0.001 TYR H 32 ARG 0.008 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 39) link_NAG-ASN : angle 2.66724 ( 117) link_BETA1-4 : bond 0.00308 ( 18) link_BETA1-4 : angle 0.99230 ( 54) hydrogen bonds : bond 0.03828 ( 870) hydrogen bonds : angle 5.02048 ( 2415) SS BOND : bond 0.00182 ( 35) SS BOND : angle 1.11251 ( 70) covalent geometry : bond 0.00291 (23472) covalent geometry : angle 0.52326 (31945) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23077.23 seconds wall clock time: 398 minutes 42.38 seconds (23922.38 seconds total)