Starting phenix.real_space_refine on Wed May 28 05:00:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328.map" model { file = "/net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itu_35328/05_2025/8itu_35328_neut.cif" } resolution = 3.68 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 19224 2.51 5 N 4932 2.21 5 O 5847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 3.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30144 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8118 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8119 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 8113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8113 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} 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: "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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 19.73, per 1000 atoms: 0.65 Number of scatterers: 30144 At special positions: 0 Unit cell: (142.68, 168.92, 205, 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 141 16.00 O 5847 8.00 N 4932 7.00 C 19224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 50 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 3.5 seconds 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 68 sheets defined 20.7% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.585A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.570A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 383 through 387' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.151A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.972A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.055A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.085A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.497A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.240A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.380A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.544A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.612A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.023A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.966A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.613A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.098A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.180A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (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: 4.498A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.554A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.451A 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 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.542A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.596A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.690A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.091A 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: 4.524A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.500A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.848A pdb=" N LYS E 66 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.716A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.067A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.863A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.892A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.896A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.760A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.549A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 6.365A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.092A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.504A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.504A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.320A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.902A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.919A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 728 removed outlier: 7.245A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.365A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.333A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.656A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.776A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.134A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.289A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.313A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.136A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.778A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.164A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.758A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.758A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.517A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.787A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.676A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.791A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.391A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.370A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.302A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.601A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.675A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.109A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.779A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.073A pdb=" N VAL D 11 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 105 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.697A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.671A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.587A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.406A pdb=" N VAL F 11 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS F 110 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU F 13 " --> pdb=" O LYS F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.591A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.521A pdb=" N LEU G 17 " --> pdb=" O MET G 83 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET G 83 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.810A pdb=" N ILE G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 60 through 61 removed outlier: 3.810A pdb=" N ILE G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.586A pdb=" N THR H 7 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.430A pdb=" N VAL H 11 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS H 110 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU H 13 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 105 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AH2, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.669A pdb=" N MET I 83 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR I 78 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.677A pdb=" N LEU I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AH5, first strand: chain 'I' and resid 49 through 50 1182 hydrogen bonds defined for protein. 3225 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: 15.38 Time building geometry restraints manager: 8.58 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: 9456 1.34 - 1.46: 6587 1.46 - 1.58: 14620 1.58 - 1.70: 0 1.70 - 1.82: 177 Bond restraints: 30840 Sorted by residual: bond pdb=" N ILE D 29 " pdb=" CA ILE D 29 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.37e+01 bond pdb=" N ARG C 328 " pdb=" CA ARG C 328 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.23e-02 6.61e+03 1.12e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.455 1.486 -0.031 9.60e-03 1.09e+04 1.07e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.20e-02 6.94e+03 9.74e+00 bond pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.22e-02 6.72e+03 9.04e+00 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 40833 1.56 - 3.12: 990 3.12 - 4.67: 119 4.67 - 6.23: 19 6.23 - 7.79: 5 Bond angle restraints: 41966 Sorted by residual: angle pdb=" N PRO C 330 " pdb=" CA PRO C 330 " pdb=" C PRO C 330 " ideal model delta sigma weight residual 111.34 118.56 -7.22 1.55e+00 4.16e-01 2.17e+01 angle pdb=" CA ARG C 328 " pdb=" C ARG C 328 " pdb=" O ARG C 328 " ideal model delta sigma weight residual 121.11 116.66 4.45 1.13e+00 7.83e-01 1.55e+01 angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 115.36 110.17 5.19 1.33e+00 5.65e-01 1.53e+01 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 112.43 108.84 3.59 9.20e-01 1.18e+00 1.52e+01 angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.27 110.07 5.20 1.41e+00 5.03e-01 1.36e+01 ... (remaining 41961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17247 17.99 - 35.98: 1327 35.98 - 53.97: 248 53.97 - 71.97: 51 71.97 - 89.96: 34 Dihedral angle restraints: 18907 sinusoidal: 7888 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.53 -75.47 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.06 -60.94 1 1.00e+01 1.00e-02 4.94e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.79 58.21 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 18904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4851 0.128 - 0.256: 24 0.256 - 0.384: 1 0.384 - 0.512: 0 0.512 - 0.640: 2 Chirality restraints: 4878 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.44e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 4875 not shown) Planarity restraints: 5376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.097 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" CG ASN C 331 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.295 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 327 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C VAL C 327 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL C 327 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG C 328 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 986 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.032 5.00e-02 4.00e+02 ... (remaining 5373 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2640 2.74 - 3.28: 30327 3.28 - 3.82: 49872 3.82 - 4.36: 57332 4.36 - 4.90: 100547 Nonbonded interactions: 240718 Sorted by model distance: nonbonded pdb=" OG SER A 247 " pdb=" OG1 THR A 259 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR I 80 " pdb=" OE1 GLN I 82 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 124 " pdb=" OD1 ASN B 125 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.243 3.040 ... (remaining 240713 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' and (resid 15 through 356 or (resid 357 and (name N or name CA or nam \ e C or name O or name CB )) or resid 358 through 579 or (resid 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 through 977 or (resid 9 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 979 through \ 993 or (resid 994 and (name N or name CA or name C or name O or name CB )) or r \ esid 995 through 1147 or resid 1301 through 1304)) selection = (chain 'B' and (resid 15 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 356 or (resid 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 827 or resid 853 t \ hrough 977 or (resid 978 and (name N or name CA or name C or name O or name CB ) \ ) or resid 979 through 1147 or resid 1301 through 1304)) selection = (chain 'C' and (resid 15 through 80 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 827 or resid 853 through 993 or (r \ esid 994 and (name N or name CA or name C or name O or name CB )) or resid 995 t \ hrough 1147 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 71.480 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30935 Z= 0.201 Angle : 0.610 25.184 42200 Z= 0.324 Chirality : 0.046 0.640 4878 Planarity : 0.004 0.058 5347 Dihedral : 13.248 89.956 11676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.09 (0.14), residues: 3737 helix: 2.05 (0.21), residues: 659 sheet: 0.41 (0.18), residues: 867 loop : -0.94 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 112 HIS 0.003 0.001 HIS C 954 PHE 0.035 0.001 PHE A 906 TYR 0.014 0.001 TYR C 396 ARG 0.005 0.000 ARG H 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 29) link_NAG-ASN : angle 4.29089 ( 87) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.01541 ( 45) hydrogen bonds : bond 0.21036 ( 1118) hydrogen bonds : angle 8.29760 ( 3225) SS BOND : bond 0.00271 ( 51) SS BOND : angle 0.86243 ( 102) covalent geometry : bond 0.00386 (30840) covalent geometry : angle 0.57720 (41966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6920 (m-90) cc_final: 0.6677 (m-90) REVERT: A 200 TYR cc_start: 0.7798 (m-10) cc_final: 0.7587 (m-80) REVERT: A 270 LEU cc_start: 0.8634 (mt) cc_final: 0.8401 (mp) REVERT: A 309 GLU cc_start: 0.7559 (mp0) cc_final: 0.7265 (mp0) REVERT: A 574 ASP cc_start: 0.7144 (t70) cc_final: 0.6453 (m-30) REVERT: A 856 LYS cc_start: 0.8480 (mppt) cc_final: 0.8261 (mmtp) REVERT: A 980 ILE cc_start: 0.8373 (mm) cc_final: 0.8149 (tp) REVERT: A 1041 ASP cc_start: 0.7829 (m-30) cc_final: 0.7567 (t0) REVERT: B 128 ILE cc_start: 0.8582 (mp) cc_final: 0.8145 (mm) REVERT: B 140 PHE cc_start: 0.6479 (p90) cc_final: 0.6007 (p90) REVERT: B 186 PHE cc_start: 0.7039 (m-80) cc_final: 0.6438 (p90) REVERT: B 206 LYS cc_start: 0.7166 (tppt) cc_final: 0.6655 (mmtt) REVERT: B 228 ASP cc_start: 0.7188 (t0) cc_final: 0.6963 (t0) REVERT: B 314 GLN cc_start: 0.8284 (tt0) cc_final: 0.8034 (tt0) REVERT: B 796 TYR cc_start: 0.6630 (t80) cc_final: 0.6164 (t80) REVERT: B 950 ASP cc_start: 0.8111 (m-30) cc_final: 0.7686 (m-30) REVERT: B 1050 MET cc_start: 0.7923 (ptt) cc_final: 0.7647 (ptt) REVERT: C 140 PHE cc_start: 0.7531 (p90) cc_final: 0.6637 (p90) REVERT: C 153 MET cc_start: 0.4193 (tmm) cc_final: 0.2955 (pmm) REVERT: C 950 ASP cc_start: 0.8045 (m-30) cc_final: 0.7826 (m-30) REVERT: C 969 LYS cc_start: 0.8791 (tppp) cc_final: 0.8392 (mmmm) REVERT: C 975 SER cc_start: 0.8736 (t) cc_final: 0.8432 (p) REVERT: D 4 MET cc_start: 0.0939 (ptp) cc_final: 0.0597 (ptp) REVERT: E 34 MET cc_start: 0.2500 (mmp) cc_final: 0.0857 (tpp) REVERT: F 4 MET cc_start: 0.1795 (ptp) cc_final: 0.1199 (mpp) REVERT: H 4 MET cc_start: 0.5737 (ttm) cc_final: 0.5207 (ptp) REVERT: H 87 TYR cc_start: 0.5339 (m-80) cc_final: 0.4921 (m-80) REVERT: H 91 THR cc_start: 0.4777 (t) cc_final: 0.3958 (t) REVERT: I 34 MET cc_start: 0.5332 (tmm) cc_final: 0.4778 (tmm) outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.4147 time to fit residues: 347.7235 Evaluate side-chains 262 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 220 optimal weight: 9.9990 chunk 343 optimal weight: 50.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 115 GLN A 188 ASN A 536 ASN A 901 GLN A 926 GLN A1002 GLN A1010 GLN B 66 HIS B 919 ASN C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 544 ASN C 804 GLN C 935 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 38 GLN H 70 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.200914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.176679 restraints weight = 69489.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.175373 restraints weight = 121155.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.175352 restraints weight = 112435.380| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30935 Z= 0.198 Angle : 0.683 14.863 42200 Z= 0.350 Chirality : 0.048 0.379 4878 Planarity : 0.005 0.067 5347 Dihedral : 6.283 59.488 4990 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer: Outliers : 1.52 % Allowed : 7.56 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.09 (0.13), residues: 3737 helix: 1.79 (0.20), residues: 680 sheet: 0.55 (0.16), residues: 976 loop : -1.03 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.006 0.001 HIS A 49 PHE 0.026 0.002 PHE A 906 TYR 0.033 0.002 TYR B1067 ARG 0.006 0.001 ARG C 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 29) link_NAG-ASN : angle 3.34018 ( 87) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.27533 ( 45) hydrogen bonds : bond 0.05638 ( 1118) hydrogen bonds : angle 6.01099 ( 3225) SS BOND : bond 0.00724 ( 51) SS BOND : angle 1.95901 ( 102) covalent geometry : bond 0.00457 (30840) covalent geometry : angle 0.65923 (41966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.8070 (mt) cc_final: 0.7830 (mp) REVERT: A 531 THR cc_start: 0.7508 (m) cc_final: 0.7221 (m) REVERT: A 1041 ASP cc_start: 0.7984 (m-30) cc_final: 0.7742 (t0) REVERT: A 1115 ILE cc_start: 0.9067 (tt) cc_final: 0.8821 (mt) REVERT: B 314 GLN cc_start: 0.8028 (tt0) cc_final: 0.7792 (tt0) REVERT: B 725 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: B 1029 MET cc_start: 0.8845 (tpp) cc_final: 0.8436 (ttm) REVERT: C 153 MET cc_start: 0.2399 (tmm) cc_final: 0.1787 (pmm) REVERT: C 975 SER cc_start: 0.8712 (t) cc_final: 0.8427 (p) REVERT: E 34 MET cc_start: 0.1622 (mmp) cc_final: 0.0626 (tpp) REVERT: E 83 MET cc_start: 0.0199 (OUTLIER) cc_final: -0.0035 (tpp) REVERT: I 71 ILE cc_start: -0.0434 (tp) cc_final: -0.0935 (mt) outliers start: 50 outliers final: 30 residues processed: 323 average time/residue: 0.3576 time to fit residues: 199.0571 Evaluate side-chains 254 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 212 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 372 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 369 optimal weight: 30.0000 chunk 199 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 66 HIS B 901 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN H 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.198709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.174357 restraints weight = 69009.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.173141 restraints weight = 128269.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.172429 restraints weight = 116771.010| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30935 Z= 0.145 Angle : 0.583 12.941 42200 Z= 0.297 Chirality : 0.045 0.311 4878 Planarity : 0.004 0.060 5347 Dihedral : 5.734 57.281 4990 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 1.68 % Allowed : 9.88 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.01 (0.14), residues: 3737 helix: 2.23 (0.21), residues: 662 sheet: 0.51 (0.16), residues: 971 loop : -1.03 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 104 HIS 0.009 0.001 HIS B 66 PHE 0.020 0.002 PHE C 329 TYR 0.024 0.001 TYR B1067 ARG 0.006 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 29) link_NAG-ASN : angle 2.82703 ( 87) link_BETA1-4 : bond 0.00395 ( 15) link_BETA1-4 : angle 1.17403 ( 45) hydrogen bonds : bond 0.05062 ( 1118) hydrogen bonds : angle 5.51999 ( 3225) SS BOND : bond 0.00384 ( 51) SS BOND : angle 1.61818 ( 102) covalent geometry : bond 0.00335 (30840) covalent geometry : angle 0.56386 (41966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8045 (tp40) cc_final: 0.7843 (tp40) REVERT: A 1041 ASP cc_start: 0.7891 (m-30) cc_final: 0.7629 (t0) REVERT: A 1115 ILE cc_start: 0.9089 (tt) cc_final: 0.8835 (mt) REVERT: B 725 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: B 1029 MET cc_start: 0.8751 (tpp) cc_final: 0.8449 (ttm) REVERT: C 1031 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: E 34 MET cc_start: 0.1813 (mmp) cc_final: 0.0896 (tpp) REVERT: F 4 MET cc_start: 0.0579 (mpp) cc_final: 0.0016 (ttp) REVERT: H 4 MET cc_start: 0.4214 (OUTLIER) cc_final: 0.3985 (ptm) REVERT: I 34 MET cc_start: 0.2238 (tmm) cc_final: 0.1990 (ttm) REVERT: I 71 ILE cc_start: -0.0365 (tp) cc_final: -0.0647 (mt) outliers start: 55 outliers final: 35 residues processed: 258 average time/residue: 0.3768 time to fit residues: 165.7134 Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 4 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 200 optimal weight: 0.9990 chunk 330 optimal weight: 0.2980 chunk 175 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 115 GLN B 755 GLN B 901 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.198749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.174392 restraints weight = 69172.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.173674 restraints weight = 114452.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.172587 restraints weight = 102481.388| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30935 Z= 0.116 Angle : 0.548 12.297 42200 Z= 0.278 Chirality : 0.044 0.239 4878 Planarity : 0.004 0.054 5347 Dihedral : 5.244 56.292 4990 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 1.92 % Allowed : 11.10 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.06 (0.14), residues: 3737 helix: 2.31 (0.21), residues: 665 sheet: 0.59 (0.17), residues: 966 loop : -1.01 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.004 0.001 HIS A 49 PHE 0.023 0.001 PHE B 329 TYR 0.023 0.001 TYR B1067 ARG 0.004 0.000 ARG C 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 29) link_NAG-ASN : angle 2.51790 ( 87) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 1.14780 ( 45) hydrogen bonds : bond 0.04413 ( 1118) hydrogen bonds : angle 5.18108 ( 3225) SS BOND : bond 0.00313 ( 51) SS BOND : angle 1.23395 ( 102) covalent geometry : bond 0.00259 (30840) covalent geometry : angle 0.53301 (41966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 965 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7919 (mm-40) REVERT: A 1041 ASP cc_start: 0.7845 (m-30) cc_final: 0.7619 (t0) REVERT: A 1115 ILE cc_start: 0.9143 (tt) cc_final: 0.8846 (mt) REVERT: B 1029 MET cc_start: 0.8752 (tpp) cc_final: 0.8430 (ttm) REVERT: C 1031 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: E 34 MET cc_start: 0.1638 (mmp) cc_final: 0.0587 (tpp) REVERT: E 35 CYS cc_start: -0.0577 (OUTLIER) cc_final: -0.0992 (p) REVERT: I 34 MET cc_start: 0.2594 (tmm) cc_final: 0.2228 (ttt) REVERT: I 71 ILE cc_start: -0.0310 (tp) cc_final: -0.0633 (mt) outliers start: 63 outliers final: 36 residues processed: 259 average time/residue: 0.3605 time to fit residues: 161.4165 Evaluate side-chains 228 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 357 optimal weight: 20.0000 chunk 175 optimal weight: 0.0010 chunk 38 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 901 GLN C 207 HIS C 901 GLN C1005 GLN C1010 GLN H 38 GLN I 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.193083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.168436 restraints weight = 67702.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.167005 restraints weight = 113544.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.164751 restraints weight = 111821.372| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30935 Z= 0.206 Angle : 0.635 10.921 42200 Z= 0.324 Chirality : 0.047 0.288 4878 Planarity : 0.004 0.053 5347 Dihedral : 5.308 57.829 4990 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.28 % Favored : 95.64 % Rotamer: Outliers : 1.89 % Allowed : 12.75 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.22 (0.14), residues: 3737 helix: 1.82 (0.20), residues: 680 sheet: 0.48 (0.17), residues: 989 loop : -1.18 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 32 HIS 0.008 0.002 HIS B 519 PHE 0.036 0.002 PHE E 69 TYR 0.025 0.002 TYR H 87 ARG 0.005 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 29) link_NAG-ASN : angle 2.82593 ( 87) link_BETA1-4 : bond 0.00247 ( 15) link_BETA1-4 : angle 1.42223 ( 45) hydrogen bonds : bond 0.05899 ( 1118) hydrogen bonds : angle 5.42983 ( 3225) SS BOND : bond 0.00485 ( 51) SS BOND : angle 1.62388 ( 102) covalent geometry : bond 0.00491 (30840) covalent geometry : angle 0.61722 (41966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7242 (tp40) REVERT: A 1041 ASP cc_start: 0.7872 (m-30) cc_final: 0.7649 (t0) REVERT: B 1002 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 1029 MET cc_start: 0.8934 (tpp) cc_final: 0.8658 (ttm) REVERT: C 207 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.5880 (t70) REVERT: E 34 MET cc_start: 0.1829 (mmp) cc_final: 0.0367 (tmm) REVERT: E 35 CYS cc_start: -0.0538 (OUTLIER) cc_final: -0.0773 (p) REVERT: E 83 MET cc_start: 0.1017 (tpp) cc_final: 0.0111 (ptp) REVERT: I 34 MET cc_start: 0.2784 (tmm) cc_final: 0.2535 (ttt) REVERT: I 71 ILE cc_start: -0.0238 (tp) cc_final: -0.0542 (mt) outliers start: 62 outliers final: 46 residues processed: 245 average time/residue: 0.3660 time to fit residues: 154.1551 Evaluate side-chains 217 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 286 optimal weight: 0.4980 chunk 239 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 206 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 284 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 66 HIS C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.183798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134461 restraints weight = 61038.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124586 restraints weight = 65299.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.118503 restraints weight = 52504.355| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30935 Z= 0.120 Angle : 0.552 9.417 42200 Z= 0.280 Chirality : 0.044 0.237 4878 Planarity : 0.004 0.051 5347 Dihedral : 5.011 57.033 4990 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.86 % Allowed : 13.24 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.03 (0.14), residues: 3737 helix: 2.16 (0.21), residues: 677 sheet: 0.55 (0.16), residues: 993 loop : -1.11 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.011 0.001 HIS C 207 PHE 0.027 0.001 PHE A 133 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 29) link_NAG-ASN : angle 2.51580 ( 87) link_BETA1-4 : bond 0.00360 ( 15) link_BETA1-4 : angle 1.23997 ( 45) hydrogen bonds : bond 0.04808 ( 1118) hydrogen bonds : angle 5.15540 ( 3225) SS BOND : bond 0.00367 ( 51) SS BOND : angle 1.38484 ( 102) covalent geometry : bond 0.00273 (30840) covalent geometry : angle 0.53609 (41966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 3.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6876 (mm) REVERT: A 1115 ILE cc_start: 0.9103 (tt) cc_final: 0.8855 (mt) REVERT: B 1029 MET cc_start: 0.8947 (tpp) cc_final: 0.8665 (ttm) REVERT: C 207 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6409 (t70) REVERT: E 34 MET cc_start: 0.2150 (mmp) cc_final: -0.0002 (tmm) REVERT: E 35 CYS cc_start: 0.0387 (OUTLIER) cc_final: -0.1171 (p) REVERT: E 83 MET cc_start: 0.1193 (tpp) cc_final: 0.0389 (ptm) REVERT: I 34 MET cc_start: 0.4441 (tmm) cc_final: 0.3950 (ttt) outliers start: 61 outliers final: 40 residues processed: 236 average time/residue: 0.3460 time to fit residues: 142.2907 Evaluate side-chains 210 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 149 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 303 optimal weight: 0.3980 chunk 367 optimal weight: 30.0000 chunk 349 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 318 optimal weight: 0.0980 chunk 265 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 66 HIS C 30 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.193803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.168901 restraints weight = 67677.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.168030 restraints weight = 117635.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.167244 restraints weight = 95946.080| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30935 Z= 0.142 Angle : 0.569 10.964 42200 Z= 0.287 Chirality : 0.044 0.228 4878 Planarity : 0.004 0.050 5347 Dihedral : 4.914 56.951 4990 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 1.89 % Allowed : 13.97 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.04 (0.14), residues: 3737 helix: 2.09 (0.21), residues: 680 sheet: 0.63 (0.16), residues: 959 loop : -1.11 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 47 HIS 0.018 0.001 HIS C 207 PHE 0.018 0.001 PHE C 541 TYR 0.027 0.001 TYR B 170 ARG 0.003 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00299 ( 29) link_NAG-ASN : angle 2.48537 ( 87) link_BETA1-4 : bond 0.00325 ( 15) link_BETA1-4 : angle 1.23914 ( 45) hydrogen bonds : bond 0.04843 ( 1118) hydrogen bonds : angle 5.08775 ( 3225) SS BOND : bond 0.00388 ( 51) SS BOND : angle 1.33390 ( 102) covalent geometry : bond 0.00330 (30840) covalent geometry : angle 0.55396 (41966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 186 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 1002 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 1029 MET cc_start: 0.8910 (tpp) cc_final: 0.8625 (ttm) REVERT: C 41 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7829 (tppt) REVERT: E 34 MET cc_start: 0.1893 (mmp) cc_final: 0.0199 (tmm) REVERT: E 83 MET cc_start: 0.1181 (tpp) cc_final: -0.0289 (ptp) REVERT: F 4 MET cc_start: 0.1197 (mpp) cc_final: -0.0604 (ttp) REVERT: H 47 LEU cc_start: 0.1561 (OUTLIER) cc_final: 0.1274 (mt) REVERT: I 34 MET cc_start: 0.2895 (tmm) cc_final: 0.2566 (ttt) outliers start: 62 outliers final: 47 residues processed: 233 average time/residue: 0.3595 time to fit residues: 146.3749 Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 67 optimal weight: 0.7980 chunk 341 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 chunk 18 optimal weight: 0.0870 chunk 295 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 66 HIS C 901 GLN I 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.195261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.169654 restraints weight = 68422.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.168924 restraints weight = 117192.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.167895 restraints weight = 108562.734| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 30935 Z= 0.108 Angle : 0.566 16.005 42200 Z= 0.283 Chirality : 0.044 0.320 4878 Planarity : 0.004 0.048 5347 Dihedral : 4.773 56.599 4990 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.65 % Allowed : 14.27 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.07 (0.14), residues: 3737 helix: 2.20 (0.21), residues: 680 sheet: 0.67 (0.17), residues: 956 loop : -1.02 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 36 HIS 0.006 0.001 HIS B 66 PHE 0.018 0.001 PHE A 981 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 29) link_NAG-ASN : angle 2.47802 ( 87) link_BETA1-4 : bond 0.00404 ( 15) link_BETA1-4 : angle 1.13205 ( 45) hydrogen bonds : bond 0.04385 ( 1118) hydrogen bonds : angle 4.96769 ( 3225) SS BOND : bond 0.00301 ( 51) SS BOND : angle 1.58119 ( 102) covalent geometry : bond 0.00242 (30840) covalent geometry : angle 0.54942 (41966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8850 (mt) REVERT: B 1029 MET cc_start: 0.8728 (tpp) cc_final: 0.8450 (ttm) REVERT: C 41 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7890 (tppt) REVERT: E 34 MET cc_start: 0.1861 (mmp) cc_final: 0.0205 (tpp) REVERT: E 83 MET cc_start: 0.0809 (tpp) cc_final: -0.0524 (ptp) REVERT: F 4 MET cc_start: 0.1066 (mpp) cc_final: -0.0624 (ttp) REVERT: H 47 LEU cc_start: 0.1918 (OUTLIER) cc_final: 0.1657 (mt) outliers start: 54 outliers final: 45 residues processed: 231 average time/residue: 0.3615 time to fit residues: 144.0964 Evaluate side-chains 226 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 134 optimal weight: 7.9990 chunk 243 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 317 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 368 optimal weight: 40.0000 chunk 247 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 926 GLN A 965 GLN B 66 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 536 ASN C 762 GLN C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.185728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.160261 restraints weight = 67154.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.157836 restraints weight = 114863.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.156830 restraints weight = 103269.078| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.116 30935 Z= 0.566 Angle : 0.991 15.004 42200 Z= 0.507 Chirality : 0.060 0.345 4878 Planarity : 0.006 0.059 5347 Dihedral : 6.813 59.727 4990 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 2.20 % Allowed : 14.39 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.13), residues: 3737 helix: 0.46 (0.19), residues: 697 sheet: 0.03 (0.17), residues: 875 loop : -1.61 (0.12), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 64 HIS 0.014 0.003 HIS A1058 PHE 0.039 0.004 PHE A 970 TYR 0.036 0.003 TYR A1067 ARG 0.013 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 29) link_NAG-ASN : angle 3.94301 ( 87) link_BETA1-4 : bond 0.00479 ( 15) link_BETA1-4 : angle 2.26472 ( 45) hydrogen bonds : bond 0.08697 ( 1118) hydrogen bonds : angle 6.25494 ( 3225) SS BOND : bond 0.00670 ( 51) SS BOND : angle 2.67200 ( 102) covalent geometry : bond 0.01382 (30840) covalent geometry : angle 0.96529 (41966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 191 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.6850 (m-10) cc_final: 0.6649 (m-10) REVERT: B 1002 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 823 PHE cc_start: 0.8288 (t80) cc_final: 0.8028 (t80) REVERT: C 988 GLU cc_start: 0.7400 (mp0) cc_final: 0.7116 (mp0) REVERT: E 34 MET cc_start: 0.2141 (mmp) cc_final: 0.1102 (tpt) REVERT: E 79 VAL cc_start: -0.3858 (OUTLIER) cc_final: -0.4275 (m) REVERT: E 83 MET cc_start: 0.1453 (tpp) cc_final: -0.0727 (ptp) REVERT: F 4 MET cc_start: 0.1385 (mpp) cc_final: -0.0488 (ttp) REVERT: H 47 LEU cc_start: 0.1894 (OUTLIER) cc_final: 0.1554 (mt) REVERT: I 34 MET cc_start: 0.2528 (tmm) cc_final: 0.2068 (tmm) outliers start: 72 outliers final: 54 residues processed: 253 average time/residue: 0.3423 time to fit residues: 149.2320 Evaluate side-chains 210 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 107 optimal weight: 0.7980 chunk 345 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 292 optimal weight: 0.8980 chunk 327 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 926 GLN A 965 GLN B 66 HIS I 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.189975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.165172 restraints weight = 66913.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164096 restraints weight = 108933.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.161905 restraints weight = 106816.942| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30935 Z= 0.192 Angle : 0.679 15.885 42200 Z= 0.342 Chirality : 0.047 0.581 4878 Planarity : 0.005 0.071 5347 Dihedral : 5.921 58.742 4990 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 1.65 % Allowed : 15.86 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3737 helix: 1.25 (0.20), residues: 703 sheet: 0.20 (0.17), residues: 914 loop : -1.40 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 104 HIS 0.006 0.001 HIS B 66 PHE 0.024 0.002 PHE A 565 TYR 0.026 0.001 TYR A1067 ARG 0.007 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 29) link_NAG-ASN : angle 3.32351 ( 87) link_BETA1-4 : bond 0.00399 ( 15) link_BETA1-4 : angle 1.64644 ( 45) hydrogen bonds : bond 0.05904 ( 1118) hydrogen bonds : angle 5.51961 ( 3225) SS BOND : bond 0.00429 ( 51) SS BOND : angle 1.65595 ( 102) covalent geometry : bond 0.00459 (30840) covalent geometry : angle 0.65656 (41966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7936 (tm-30) REVERT: C 823 PHE cc_start: 0.7970 (t80) cc_final: 0.7722 (t80) REVERT: E 34 MET cc_start: 0.1764 (mmp) cc_final: 0.0120 (tpt) REVERT: E 79 VAL cc_start: -0.3947 (OUTLIER) cc_final: -0.4348 (m) REVERT: E 83 MET cc_start: 0.1143 (tpp) cc_final: -0.0785 (ptp) REVERT: H 47 LEU cc_start: 0.1563 (OUTLIER) cc_final: 0.1279 (mt) REVERT: I 34 MET cc_start: 0.2508 (tmm) cc_final: 0.2015 (tmm) outliers start: 54 outliers final: 42 residues processed: 206 average time/residue: 0.3594 time to fit residues: 129.8251 Evaluate side-chains 191 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 157 optimal weight: 0.6980 chunk 371 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 330 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 965 GLN B 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.190457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.166263 restraints weight = 67240.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.164345 restraints weight = 104272.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.162187 restraints weight = 106944.990| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30935 Z= 0.158 Angle : 0.648 15.870 42200 Z= 0.326 Chirality : 0.046 0.419 4878 Planarity : 0.004 0.075 5347 Dihedral : 5.790 58.157 4990 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 1.62 % Allowed : 15.95 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.58 (0.13), residues: 3737 helix: 1.38 (0.20), residues: 709 sheet: 0.27 (0.17), residues: 904 loop : -1.35 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.007 0.001 HIS B 66 PHE 0.042 0.002 PHE A 392 TYR 0.023 0.001 TYR B1067 ARG 0.012 0.000 ARG I 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 29) link_NAG-ASN : angle 3.12130 ( 87) link_BETA1-4 : bond 0.00385 ( 15) link_BETA1-4 : angle 1.55846 ( 45) hydrogen bonds : bond 0.05662 ( 1118) hydrogen bonds : angle 5.40389 ( 3225) SS BOND : bond 0.00390 ( 51) SS BOND : angle 1.61391 ( 102) covalent geometry : bond 0.00377 (30840) covalent geometry : angle 0.62672 (41966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8320.40 seconds wall clock time: 148 minutes 10.19 seconds (8890.19 seconds total)