Starting phenix.real_space_refine on Sat May 24 12:31:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlt_27515/05_2025/8dlt_27515.cif" } resolution = 2.4 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= -0.001 sd= 0.038 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 111 5.16 5 C 16059 2.51 5 N 4137 2.21 5 O 4938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25245 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8135 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "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: "H" 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 16.03, per 1000 atoms: 0.63 Number of scatterers: 25245 At special positions: 0 Unit cell: (140, 146, 197, 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 111 16.00 O 4938 8.00 N 4137 7.00 C 16059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.04 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 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 H 1 " - " NAG H 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " 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 H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 3.2 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 25.1% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.599A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.815A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.643A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.015A 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: 3.571A 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 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.035A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.999A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.556A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1147' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.153A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.817A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.544A 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 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.997A 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 1033 removed outlier: 3.736A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.612A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.805A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.658A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.701A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.838A 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 616 through 620 removed outlier: 3.973A 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: 3.602A 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 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.103A 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 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 1033 removed outlier: 4.062A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.212A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.240A 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: 6.088A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.081A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 3.668A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.968A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.931A 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: 5.285A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.933A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.098A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.611A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 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: 3.756A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.197A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.581A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.119A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 3.929A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.683A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.096A 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=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.009A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.885A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.768A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.484A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, 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: 3.791A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.232A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.734A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 78 through 79 current: chain 'C' and resid 189 through 197 removed outlier: 6.377A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 removed outlier: 3.622A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.844A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.876A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.101A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.579A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.168A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, 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: 3.777A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.137A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 917 hydrogen bonds defined for protein. 2526 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: 12.08 Time building geometry restraints manager: 7.84 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: 7985 1.34 - 1.47: 6384 1.47 - 1.59: 11305 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25812 Sorted by residual: bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.80e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.92e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.66e+00 ... (remaining 25807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 34320 2.27 - 4.54: 733 4.54 - 6.81: 60 6.81 - 9.09: 17 9.09 - 11.36: 3 Bond angle restraints: 35133 Sorted by residual: angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.78 -5.08 1.22e+00 6.72e-01 1.73e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.63 -4.93 1.22e+00 6.72e-01 1.64e+01 angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 122.59 -4.66 1.20e+00 6.94e-01 1.51e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 ... (remaining 35128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14921 17.89 - 35.78: 990 35.78 - 53.67: 185 53.67 - 71.57: 53 71.57 - 89.46: 30 Dihedral angle restraints: 16179 sinusoidal: 7101 harmonic: 9078 Sorted by residual: dihedral pdb=" CA CYS B 379 " pdb=" C CYS B 379 " pdb=" N TYR B 380 " pdb=" CA TYR B 380 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PHE C 392 " pdb=" C PHE C 392 " pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR B 599 " pdb=" C THR B 599 " pdb=" N PRO B 600 " pdb=" CA PRO B 600 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3519 0.078 - 0.156: 596 0.156 - 0.234: 35 0.234 - 0.312: 3 0.312 - 0.391: 2 Chirality restraints: 4155 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+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 -2.08 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4152 not shown) Planarity restraints: 4521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.020 2.00e-02 2.50e+03 2.25e-02 8.87e+00 pdb=" CG PHE A 906 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B1029 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C MET B1029 " -0.048 2.00e-02 2.50e+03 pdb=" O MET B1029 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B1030 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C1029 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C MET C1029 " 0.046 2.00e-02 2.50e+03 pdb=" O MET C1029 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C1030 " -0.015 2.00e-02 2.50e+03 ... (remaining 4518 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2407 2.76 - 3.29: 23171 3.29 - 3.83: 42958 3.83 - 4.36: 50127 4.36 - 4.90: 86249 Nonbonded interactions: 204912 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.263 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.290 3.040 nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.298 3.040 ... (remaining 204907 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' 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' } 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 60.420 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.190 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:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 0.105 25914 Z= 0.237 Angle : 0.791 15.189 35397 Z= 0.407 Chirality : 0.055 0.391 4155 Planarity : 0.005 0.059 4479 Dihedral : 12.931 89.456 10209 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.21 (0.15), residues: 3072 helix: 1.57 (0.20), residues: 663 sheet: 0.59 (0.20), residues: 634 loop : -0.59 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 886 HIS 0.006 0.001 HIS C1048 PHE 0.052 0.002 PHE A 906 TYR 0.021 0.002 TYR A 200 ARG 0.008 0.001 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 42) link_NAG-ASN : angle 3.36388 ( 126) link_BETA1-4 : bond 0.00709 ( 18) link_BETA1-4 : angle 1.31271 ( 54) hydrogen bonds : bond 0.19326 ( 917) hydrogen bonds : angle 8.09866 ( 2526) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.12690 ( 84) covalent geometry : bond 0.00510 (25812) covalent geometry : angle 0.76479 (35133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: B 229 LEU cc_start: 0.8127 (mm) cc_final: 0.7899 (mt) REVERT: B 237 ARG cc_start: 0.8461 (mmt90) cc_final: 0.8151 (mmm-85) REVERT: B 238 PHE cc_start: 0.7233 (p90) cc_final: 0.6764 (p90) REVERT: B 394 ASN cc_start: 0.6626 (m-40) cc_final: 0.6189 (p0) REVERT: B 565 PHE cc_start: 0.8374 (p90) cc_final: 0.7880 (p90) REVERT: B 985 ASP cc_start: 0.8127 (p0) cc_final: 0.7611 (p0) REVERT: C 189 LEU cc_start: 0.8183 (tp) cc_final: 0.7931 (tp) REVERT: C 351 TYR cc_start: 0.8938 (p90) cc_final: 0.8015 (p90) REVERT: C 453 TYR cc_start: 0.8521 (p90) cc_final: 0.7969 (p90) REVERT: C 697 MET cc_start: 0.8818 (ptm) cc_final: 0.8615 (ptm) REVERT: C 1145 LEU cc_start: 0.7401 (pt) cc_final: 0.6914 (tm) outliers start: 0 outliers final: 1 residues processed: 190 average time/residue: 1.2455 time to fit residues: 278.1969 Evaluate side-chains 111 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 569 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN B 69 HIS B 755 GLN B 955 ASN B1011 GLN C 394 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.111013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066126 restraints weight = 64089.404| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.28 r_work: 0.2965 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25914 Z= 0.228 Angle : 0.623 19.493 35397 Z= 0.305 Chirality : 0.046 0.301 4155 Planarity : 0.004 0.049 4479 Dihedral : 6.904 53.943 4607 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.80 % Allowed : 4.87 % Favored : 94.33 % 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: 0.32 (0.15), residues: 3072 helix: 1.97 (0.20), residues: 654 sheet: 0.45 (0.20), residues: 662 loop : -0.55 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.005 0.001 HIS B 66 PHE 0.028 0.001 PHE A 906 TYR 0.017 0.001 TYR B 265 ARG 0.004 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 42) link_NAG-ASN : angle 3.30252 ( 126) link_BETA1-4 : bond 0.00255 ( 18) link_BETA1-4 : angle 1.21941 ( 54) hydrogen bonds : bond 0.04873 ( 917) hydrogen bonds : angle 6.21989 ( 2526) SS BOND : bond 0.00216 ( 42) SS BOND : angle 0.69479 ( 84) covalent geometry : bond 0.00521 (25812) covalent geometry : angle 0.59002 (35133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6314 (t70) cc_final: 0.6080 (t70) REVERT: B 237 ARG cc_start: 0.8474 (mmt90) cc_final: 0.8201 (mmm-85) REVERT: B 238 PHE cc_start: 0.7124 (p90) cc_final: 0.6604 (p90) REVERT: B 421 TYR cc_start: 0.8333 (m-80) cc_final: 0.7855 (m-80) REVERT: B 985 ASP cc_start: 0.8593 (p0) cc_final: 0.8064 (p0) REVERT: B 990 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 189 LEU cc_start: 0.8274 (tp) cc_final: 0.7923 (tp) REVERT: C 237 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6906 (ttp-170) REVERT: C 351 TYR cc_start: 0.9170 (p90) cc_final: 0.8242 (p90) REVERT: C 378 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8259 (mmtp) REVERT: C 452 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: C 453 TYR cc_start: 0.8174 (p90) cc_final: 0.7873 (p90) REVERT: C 456 PHE cc_start: 0.8609 (m-80) cc_final: 0.8309 (m-80) REVERT: C 490 PHE cc_start: 0.8180 (t80) cc_final: 0.7973 (t80) REVERT: C 697 MET cc_start: 0.9319 (ptm) cc_final: 0.9116 (ptm) outliers start: 22 outliers final: 9 residues processed: 133 average time/residue: 1.1839 time to fit residues: 187.7440 Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 309 optimal weight: 0.1980 chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.111899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.067202 restraints weight = 63817.494| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.28 r_work: 0.2996 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25914 Z= 0.129 Angle : 0.532 11.043 35397 Z= 0.262 Chirality : 0.044 0.291 4155 Planarity : 0.004 0.040 4479 Dihedral : 6.101 53.077 4605 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.88 % Allowed : 6.04 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3072 helix: 2.21 (0.20), residues: 660 sheet: 0.40 (0.20), residues: 693 loop : -0.42 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 PHE 0.022 0.001 PHE C 168 TYR 0.015 0.001 TYR B1067 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 42) link_NAG-ASN : angle 2.75109 ( 126) link_BETA1-4 : bond 0.00341 ( 18) link_BETA1-4 : angle 1.02491 ( 54) hydrogen bonds : bond 0.04208 ( 917) hydrogen bonds : angle 5.76723 ( 2526) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.60238 ( 84) covalent geometry : bond 0.00289 (25812) covalent geometry : angle 0.50590 (35133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6240 (t70) cc_final: 0.5982 (t70) REVERT: A 990 GLU cc_start: 0.8862 (tt0) cc_final: 0.8541 (mt-10) REVERT: B 153 MET cc_start: 0.4968 (ppp) cc_final: 0.4663 (ppp) REVERT: B 237 ARG cc_start: 0.8520 (mmt90) cc_final: 0.8246 (mmm-85) REVERT: B 238 PHE cc_start: 0.7036 (p90) cc_final: 0.6437 (p90) REVERT: B 421 TYR cc_start: 0.8334 (m-80) cc_final: 0.7834 (m-80) REVERT: B 456 PHE cc_start: 0.6867 (m-80) cc_final: 0.6577 (m-80) REVERT: B 985 ASP cc_start: 0.8566 (p0) cc_final: 0.8041 (p0) REVERT: B 990 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 83 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7215 (p) REVERT: C 189 LEU cc_start: 0.8347 (tp) cc_final: 0.7992 (tp) REVERT: C 237 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7123 (ttp-170) REVERT: C 351 TYR cc_start: 0.9144 (p90) cc_final: 0.8306 (p90) REVERT: C 378 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8280 (mmtp) REVERT: C 452 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7526 (ttp80) REVERT: C 456 PHE cc_start: 0.8672 (m-80) cc_final: 0.8369 (m-80) outliers start: 24 outliers final: 7 residues processed: 131 average time/residue: 1.1758 time to fit residues: 184.5434 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 190 optimal weight: 0.0270 chunk 231 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.111144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066087 restraints weight = 64439.590| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.44 r_work: 0.2975 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25914 Z= 0.167 Angle : 0.544 15.325 35397 Z= 0.266 Chirality : 0.044 0.288 4155 Planarity : 0.003 0.040 4479 Dihedral : 5.750 55.392 4605 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.13 % Allowed : 7.35 % Favored : 91.51 % 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: 3072 helix: 2.26 (0.20), residues: 665 sheet: 0.32 (0.19), residues: 715 loop : -0.39 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS B 66 PHE 0.020 0.001 PHE C 342 TYR 0.016 0.001 TYR B1067 ARG 0.007 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 42) link_NAG-ASN : angle 2.94713 ( 126) link_BETA1-4 : bond 0.00253 ( 18) link_BETA1-4 : angle 1.07192 ( 54) hydrogen bonds : bond 0.04210 ( 917) hydrogen bonds : angle 5.58363 ( 2526) SS BOND : bond 0.00188 ( 42) SS BOND : angle 0.61066 ( 84) covalent geometry : bond 0.00379 (25812) covalent geometry : angle 0.51418 (35133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6138 (t70) cc_final: 0.5871 (t70) REVERT: A 990 GLU cc_start: 0.8899 (tt0) cc_final: 0.8599 (mt-10) REVERT: B 53 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7966 (t70) REVERT: B 153 MET cc_start: 0.4749 (ppp) cc_final: 0.4475 (ppp) REVERT: B 237 ARG cc_start: 0.8497 (mmt90) cc_final: 0.8146 (mmm-85) REVERT: B 238 PHE cc_start: 0.7073 (p90) cc_final: 0.6384 (p90) REVERT: B 269 TYR cc_start: 0.8454 (m-80) cc_final: 0.7991 (m-80) REVERT: B 421 TYR cc_start: 0.8338 (m-10) cc_final: 0.7841 (m-80) REVERT: B 456 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: B 985 ASP cc_start: 0.8608 (p0) cc_final: 0.8307 (p0) REVERT: B 990 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 83 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7272 (p) REVERT: C 189 LEU cc_start: 0.8348 (tp) cc_final: 0.7987 (tp) REVERT: C 237 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7211 (ttp-170) REVERT: C 351 TYR cc_start: 0.9159 (p90) cc_final: 0.8222 (p90) REVERT: C 378 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8367 (mmtp) REVERT: C 452 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7836 (mtp-110) REVERT: C 456 PHE cc_start: 0.8722 (m-80) cc_final: 0.8450 (m-80) REVERT: C 900 MET cc_start: 0.9559 (OUTLIER) cc_final: 0.9313 (mtp) outliers start: 31 outliers final: 9 residues processed: 131 average time/residue: 1.0481 time to fit residues: 166.6430 Evaluate side-chains 119 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.109571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.064503 restraints weight = 64357.186| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.26 r_work: 0.2931 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25914 Z= 0.272 Angle : 0.603 15.222 35397 Z= 0.295 Chirality : 0.047 0.429 4155 Planarity : 0.004 0.040 4479 Dihedral : 5.873 59.151 4605 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.91 % Allowed : 8.38 % Favored : 90.71 % 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: 0.34 (0.15), residues: 3072 helix: 2.02 (0.20), residues: 676 sheet: 0.12 (0.19), residues: 691 loop : -0.43 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.003 0.001 HIS A1088 PHE 0.021 0.001 PHE C 168 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 42) link_NAG-ASN : angle 2.99404 ( 126) link_BETA1-4 : bond 0.00262 ( 18) link_BETA1-4 : angle 1.12715 ( 54) hydrogen bonds : bond 0.04677 ( 917) hydrogen bonds : angle 5.71438 ( 2526) SS BOND : bond 0.00262 ( 42) SS BOND : angle 0.69681 ( 84) covalent geometry : bond 0.00622 (25812) covalent geometry : angle 0.57580 (35133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6181 (t70) cc_final: 0.5879 (t70) REVERT: A 990 GLU cc_start: 0.8917 (tt0) cc_final: 0.8621 (mt-10) REVERT: B 53 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8030 (t70) REVERT: B 153 MET cc_start: 0.4868 (ppp) cc_final: 0.4647 (ppp) REVERT: B 237 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8204 (mmm-85) REVERT: B 238 PHE cc_start: 0.7297 (p90) cc_final: 0.6515 (p90) REVERT: B 269 TYR cc_start: 0.8370 (m-80) cc_final: 0.8084 (m-80) REVERT: B 380 TYR cc_start: 0.8949 (m-80) cc_final: 0.8725 (m-80) REVERT: B 421 TYR cc_start: 0.8341 (m-10) cc_final: 0.8080 (m-80) REVERT: B 456 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: B 990 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 1029 MET cc_start: 0.9588 (tpp) cc_final: 0.9258 (tpp) REVERT: C 83 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7290 (p) REVERT: C 189 LEU cc_start: 0.8434 (tp) cc_final: 0.8101 (tp) REVERT: C 378 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8376 (mmtp) REVERT: C 456 PHE cc_start: 0.8734 (m-80) cc_final: 0.8475 (m-80) outliers start: 25 outliers final: 13 residues processed: 124 average time/residue: 1.1167 time to fit residues: 167.9448 Evaluate side-chains 114 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 108 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 GLN B1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.110677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.064986 restraints weight = 63771.085| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.42 r_work: 0.2971 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25914 Z= 0.142 Angle : 0.531 13.754 35397 Z= 0.260 Chirality : 0.045 0.398 4155 Planarity : 0.003 0.042 4479 Dihedral : 5.548 59.682 4605 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.02 % Allowed : 8.64 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3072 helix: 2.24 (0.21), residues: 666 sheet: 0.12 (0.19), residues: 712 loop : -0.35 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 PHE 0.025 0.001 PHE A 168 TYR 0.015 0.001 TYR B1067 ARG 0.010 0.000 ARG C 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 42) link_NAG-ASN : angle 2.76663 ( 126) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 0.95270 ( 54) hydrogen bonds : bond 0.04067 ( 917) hydrogen bonds : angle 5.50497 ( 2526) SS BOND : bond 0.00212 ( 42) SS BOND : angle 0.65194 ( 84) covalent geometry : bond 0.00319 (25812) covalent geometry : angle 0.50382 (35133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6190 (t70) cc_final: 0.5922 (t70) REVERT: A 990 GLU cc_start: 0.8903 (tt0) cc_final: 0.8605 (mt-10) REVERT: B 53 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8014 (t70) REVERT: B 153 MET cc_start: 0.4680 (ppp) cc_final: 0.4467 (ppp) REVERT: B 237 ARG cc_start: 0.8557 (mmt90) cc_final: 0.8137 (mmm-85) REVERT: B 238 PHE cc_start: 0.7240 (p90) cc_final: 0.6484 (p90) REVERT: B 269 TYR cc_start: 0.8334 (m-80) cc_final: 0.8050 (m-80) REVERT: B 421 TYR cc_start: 0.8317 (m-10) cc_final: 0.8086 (m-80) REVERT: B 456 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.6599 (m-80) REVERT: B 990 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8179 (tm-30) REVERT: C 83 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7241 (p) REVERT: C 189 LEU cc_start: 0.8419 (tp) cc_final: 0.8071 (tp) REVERT: C 378 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8477 (mmtp) REVERT: C 456 PHE cc_start: 0.8740 (m-80) cc_final: 0.8472 (m-80) REVERT: C 508 TYR cc_start: 0.8980 (m-10) cc_final: 0.8425 (m-80) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 1.0540 time to fit residues: 160.1218 Evaluate side-chains 116 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 179 optimal weight: 0.1980 chunk 270 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 288 optimal weight: 0.5980 chunk 251 optimal weight: 0.1980 chunk 215 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.110730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.066329 restraints weight = 64218.190| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.15 r_work: 0.2969 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25914 Z= 0.148 Angle : 0.533 13.531 35397 Z= 0.260 Chirality : 0.045 0.385 4155 Planarity : 0.003 0.040 4479 Dihedral : 5.280 59.015 4605 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.84 % Allowed : 9.29 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3072 helix: 2.27 (0.20), residues: 667 sheet: 0.16 (0.19), residues: 705 loop : -0.34 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 PHE 0.024 0.001 PHE C 168 TYR 0.015 0.001 TYR B1067 ARG 0.012 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 42) link_NAG-ASN : angle 2.72337 ( 126) link_BETA1-4 : bond 0.00269 ( 18) link_BETA1-4 : angle 0.99333 ( 54) hydrogen bonds : bond 0.04019 ( 917) hydrogen bonds : angle 5.42740 ( 2526) SS BOND : bond 0.00233 ( 42) SS BOND : angle 0.89233 ( 84) covalent geometry : bond 0.00336 (25812) covalent geometry : angle 0.50637 (35133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6144 (t70) cc_final: 0.5903 (t70) REVERT: A 990 GLU cc_start: 0.8864 (tt0) cc_final: 0.8561 (mt-10) REVERT: B 53 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8034 (t70) REVERT: B 237 ARG cc_start: 0.8583 (mmt90) cc_final: 0.8156 (mmm-85) REVERT: B 238 PHE cc_start: 0.7198 (p90) cc_final: 0.6464 (p90) REVERT: B 269 TYR cc_start: 0.8376 (m-80) cc_final: 0.8095 (m-80) REVERT: B 421 TYR cc_start: 0.8330 (m-10) cc_final: 0.8067 (m-80) REVERT: B 456 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6608 (m-80) REVERT: B 990 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 83 VAL cc_start: 0.7517 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 189 LEU cc_start: 0.8404 (tp) cc_final: 0.8041 (tp) REVERT: C 378 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8489 (mmtp) REVERT: C 456 PHE cc_start: 0.8778 (m-80) cc_final: 0.8506 (m-80) REVERT: C 508 TYR cc_start: 0.8929 (m-10) cc_final: 0.8366 (m-80) outliers start: 23 outliers final: 15 residues processed: 120 average time/residue: 1.0286 time to fit residues: 150.9434 Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 252 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 267 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 155 optimal weight: 0.0020 chunk 147 optimal weight: 0.5980 chunk 37 optimal weight: 30.0000 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.110817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066489 restraints weight = 64051.739| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.17 r_work: 0.2971 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25914 Z= 0.139 Angle : 0.533 13.375 35397 Z= 0.259 Chirality : 0.044 0.374 4155 Planarity : 0.003 0.039 4479 Dihedral : 5.080 55.666 4605 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.99 % Allowed : 9.29 % Favored : 89.72 % 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: 0.55 (0.15), residues: 3072 helix: 2.30 (0.20), residues: 668 sheet: 0.22 (0.19), residues: 694 loop : -0.33 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.003 0.000 HIS B 66 PHE 0.020 0.001 PHE A 168 TYR 0.016 0.001 TYR B1067 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 42) link_NAG-ASN : angle 2.68676 ( 126) link_BETA1-4 : bond 0.00278 ( 18) link_BETA1-4 : angle 0.98357 ( 54) hydrogen bonds : bond 0.03928 ( 917) hydrogen bonds : angle 5.37297 ( 2526) SS BOND : bond 0.00204 ( 42) SS BOND : angle 0.78587 ( 84) covalent geometry : bond 0.00316 (25812) covalent geometry : angle 0.50762 (35133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7660 (t60) cc_final: 0.7244 (t60) REVERT: A 66 HIS cc_start: 0.6138 (t70) cc_final: 0.5908 (t70) REVERT: A 990 GLU cc_start: 0.8874 (tt0) cc_final: 0.8579 (mt-10) REVERT: B 53 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8018 (t70) REVERT: B 237 ARG cc_start: 0.8631 (mmt90) cc_final: 0.8199 (mmm-85) REVERT: B 238 PHE cc_start: 0.7166 (p90) cc_final: 0.6435 (p90) REVERT: B 269 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: B 421 TYR cc_start: 0.8312 (m-10) cc_final: 0.8058 (m-80) REVERT: B 456 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: B 990 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 189 LEU cc_start: 0.8387 (tp) cc_final: 0.8011 (tp) REVERT: C 378 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8560 (mmtp) REVERT: C 456 PHE cc_start: 0.8769 (m-80) cc_final: 0.8497 (m-80) REVERT: C 508 TYR cc_start: 0.8924 (m-10) cc_final: 0.8351 (m-80) REVERT: C 531 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8639 (p) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 0.9998 time to fit residues: 146.9527 Evaluate side-chains 118 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 181 optimal weight: 0.6980 chunk 191 optimal weight: 0.5980 chunk 102 optimal weight: 0.0060 chunk 171 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 overall best weight: 0.4012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN C 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.111966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067741 restraints weight = 64036.963| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.30 r_work: 0.3016 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25914 Z= 0.093 Angle : 0.514 13.169 35397 Z= 0.249 Chirality : 0.044 0.355 4155 Planarity : 0.003 0.039 4479 Dihedral : 4.690 53.655 4605 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.66 % Allowed : 9.66 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3072 helix: 2.45 (0.21), residues: 667 sheet: 0.25 (0.19), residues: 708 loop : -0.24 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.005 0.000 HIS B 66 PHE 0.026 0.001 PHE C 168 TYR 0.011 0.001 TYR C1067 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 42) link_NAG-ASN : angle 2.59887 ( 126) link_BETA1-4 : bond 0.00363 ( 18) link_BETA1-4 : angle 0.91090 ( 54) hydrogen bonds : bond 0.03529 ( 917) hydrogen bonds : angle 5.17052 ( 2526) SS BOND : bond 0.00203 ( 42) SS BOND : angle 0.71101 ( 84) covalent geometry : bond 0.00206 (25812) covalent geometry : angle 0.48976 (35133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 2.621 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8937 (mt) cc_final: 0.8697 (mp) REVERT: A 571 ASP cc_start: 0.8811 (t70) cc_final: 0.8596 (t0) REVERT: A 990 GLU cc_start: 0.8829 (tt0) cc_final: 0.8548 (mt-10) REVERT: B 53 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7991 (t70) REVERT: B 237 ARG cc_start: 0.8542 (mmt90) cc_final: 0.8109 (mmm-85) REVERT: B 238 PHE cc_start: 0.7050 (p90) cc_final: 0.6342 (p90) REVERT: B 269 TYR cc_start: 0.8307 (m-80) cc_final: 0.8066 (m-80) REVERT: B 421 TYR cc_start: 0.8325 (m-10) cc_final: 0.8033 (m-80) REVERT: B 571 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7409 (p0) REVERT: B 990 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8101 (tm-30) REVERT: C 189 LEU cc_start: 0.8395 (tp) cc_final: 0.8000 (tp) REVERT: C 378 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8518 (mmtp) REVERT: C 453 TYR cc_start: 0.8273 (p90) cc_final: 0.7866 (p90) REVERT: C 456 PHE cc_start: 0.8801 (m-80) cc_final: 0.8540 (m-80) REVERT: C 508 TYR cc_start: 0.8926 (m-10) cc_final: 0.8377 (m-80) REVERT: C 531 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8727 (p) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 1.0248 time to fit residues: 162.7512 Evaluate side-chains 121 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 chunk 281 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.111391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066116 restraints weight = 63846.073| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.63 r_work: 0.2992 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25914 Z= 0.120 Angle : 0.522 13.285 35397 Z= 0.254 Chirality : 0.044 0.350 4155 Planarity : 0.003 0.039 4479 Dihedral : 4.609 52.754 4605 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.55 % Allowed : 10.06 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3072 helix: 2.49 (0.20), residues: 666 sheet: 0.30 (0.19), residues: 695 loop : -0.24 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.000 HIS A 66 PHE 0.013 0.001 PHE A 898 TYR 0.015 0.001 TYR C 453 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 42) link_NAG-ASN : angle 2.61834 ( 126) link_BETA1-4 : bond 0.00291 ( 18) link_BETA1-4 : angle 0.98234 ( 54) hydrogen bonds : bond 0.03690 ( 917) hydrogen bonds : angle 5.18023 ( 2526) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.68572 ( 84) covalent geometry : bond 0.00273 (25812) covalent geometry : angle 0.49730 (35133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 3.050 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8948 (mt) cc_final: 0.8711 (mp) REVERT: A 571 ASP cc_start: 0.8827 (t70) cc_final: 0.8546 (t0) REVERT: A 990 GLU cc_start: 0.8878 (tt0) cc_final: 0.8602 (mt-10) REVERT: B 53 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8003 (t70) REVERT: B 237 ARG cc_start: 0.8555 (mmt90) cc_final: 0.8130 (mmm-85) REVERT: B 238 PHE cc_start: 0.7131 (p90) cc_final: 0.6404 (p90) REVERT: B 269 TYR cc_start: 0.8293 (m-80) cc_final: 0.8037 (m-80) REVERT: B 421 TYR cc_start: 0.8320 (m-10) cc_final: 0.8076 (m-80) REVERT: B 990 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8231 (tm-30) REVERT: C 189 LEU cc_start: 0.8388 (tp) cc_final: 0.7968 (tp) REVERT: C 378 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8542 (mmtp) REVERT: C 453 TYR cc_start: 0.8107 (p90) cc_final: 0.7608 (p90) REVERT: C 456 PHE cc_start: 0.8760 (m-80) cc_final: 0.8521 (m-80) REVERT: C 508 TYR cc_start: 0.8913 (m-10) cc_final: 0.8360 (m-80) REVERT: C 531 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8717 (p) outliers start: 15 outliers final: 11 residues processed: 127 average time/residue: 1.0975 time to fit residues: 169.1944 Evaluate side-chains 122 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 8 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 304 optimal weight: 0.9990 chunk 276 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.111273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.067128 restraints weight = 63943.191| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.15 r_work: 0.2990 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25914 Z= 0.124 Angle : 0.529 13.336 35397 Z= 0.257 Chirality : 0.044 0.348 4155 Planarity : 0.003 0.039 4479 Dihedral : 4.560 52.719 4605 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.62 % Allowed : 10.03 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3072 helix: 2.48 (0.20), residues: 667 sheet: 0.33 (0.19), residues: 688 loop : -0.23 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.002 0.000 HIS A 207 PHE 0.025 0.001 PHE C 168 TYR 0.026 0.001 TYR B 473 ARG 0.009 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 42) link_NAG-ASN : angle 2.62159 ( 126) link_BETA1-4 : bond 0.00295 ( 18) link_BETA1-4 : angle 0.97341 ( 54) hydrogen bonds : bond 0.03709 ( 917) hydrogen bonds : angle 5.17961 ( 2526) SS BOND : bond 0.00176 ( 42) SS BOND : angle 0.67275 ( 84) covalent geometry : bond 0.00282 (25812) covalent geometry : angle 0.50469 (35133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32388.94 seconds wall clock time: 555 minutes 26.66 seconds (33326.66 seconds total)