Starting phenix.real_space_refine on Thu Jun 26 07:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itu_35328/06_2025/8itu_35328_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itu_35328/06_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_35328/06_2025/8itu_35328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itu_35328/06_2025/8itu_35328.map" model { file = "/net/cci-nas-00/data/ceres_data/8itu_35328/06_2025/8itu_35328_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itu_35328/06_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): 2.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.66, per 1000 atoms: 0.62 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: 7.10 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: 4.43 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: 14.02 Time building geometry restraints manager: 8.51 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: 9.110 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: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 69.670 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.180 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.350 ------------------------------------------------------------------------------- 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 : 3.375 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: 0.4346 time to fit residues: 364.3350 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 : 3.024 ------------------------------------------------------------------------------- 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 = 0.176678 restraints weight = 69489.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.175447 restraints weight = 121214.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.175192 restraints weight = 110459.121| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 14.862 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 0.00723 ( 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 : 3.101 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: 0.8074 (mt) cc_final: 0.7834 (mp) REVERT: A 531 THR cc_start: 0.7517 (m) cc_final: 0.7229 (m) REVERT: A 1041 ASP cc_start: 0.7975 (m-30) cc_final: 0.7737 (t0) REVERT: A 1115 ILE cc_start: 0.9053 (tt) cc_final: 0.8818 (mt) REVERT: B 314 GLN cc_start: 0.8023 (tt0) cc_final: 0.7788 (tt0) REVERT: B 725 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: B 1029 MET cc_start: 0.8841 (tpp) cc_final: 0.8437 (ttm) REVERT: C 153 MET cc_start: 0.2405 (tmm) cc_final: 0.1790 (pmm) REVERT: C 975 SER cc_start: 0.8714 (t) cc_final: 0.8425 (p) REVERT: E 34 MET cc_start: 0.1623 (mmp) cc_final: 0.0622 (tpp) REVERT: E 83 MET cc_start: 0.0205 (OUTLIER) cc_final: -0.0036 (tpp) REVERT: I 71 ILE cc_start: -0.0433 (tp) cc_final: -0.0934 (mt) outliers start: 50 outliers final: 30 residues processed: 323 average time/residue: 0.3674 time to fit residues: 201.2264 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 : 3.046 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 257 optimal weight: 7.9990 chunk 369 optimal weight: 30.0000 chunk 199 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 269 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 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 = 0.4599 r_free = 0.4599 target = 0.198604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.174900 restraints weight = 68981.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.174213 restraints weight = 119127.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.172310 restraints weight = 106003.680| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30935 Z= 0.149 Angle : 0.583 12.624 42200 Z= 0.298 Chirality : 0.045 0.318 4878 Planarity : 0.004 0.060 5347 Dihedral : 5.712 57.056 4990 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Rotamer: Outliers : 1.68 % Allowed : 9.91 % Favored : 88.41 % 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: 0.52 (0.16), residues: 972 loop : -1.05 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.009 0.001 HIS B 66 PHE 0.022 0.002 PHE C 329 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG B 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 29) link_NAG-ASN : angle 2.80513 ( 87) link_BETA1-4 : bond 0.00343 ( 15) link_BETA1-4 : angle 1.17623 ( 45) hydrogen bonds : bond 0.05026 ( 1118) hydrogen bonds : angle 5.50417 ( 3225) SS BOND : bond 0.00359 ( 51) SS BOND : angle 1.57680 ( 102) covalent geometry : bond 0.00336 (30840) covalent geometry : angle 0.56415 (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 : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1041 ASP cc_start: 0.7852 (m-30) cc_final: 0.7586 (t0) REVERT: A 1115 ILE cc_start: 0.9086 (tt) cc_final: 0.8827 (mt) REVERT: B 725 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 902 MET cc_start: 0.8596 (mmm) cc_final: 0.8377 (tpt) REVERT: B 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8440 (ttm) REVERT: C 1031 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: E 34 MET cc_start: 0.1813 (mmp) cc_final: 0.0900 (tpp) REVERT: F 4 MET cc_start: 0.0453 (mpp) cc_final: 0.0061 (ttp) REVERT: H 4 MET cc_start: 0.4223 (OUTLIER) cc_final: 0.3950 (ptm) REVERT: I 71 ILE cc_start: -0.0359 (tp) cc_final: -0.0635 (mt) outliers start: 55 outliers final: 34 residues processed: 258 average time/residue: 0.3764 time to fit residues: 163.7849 Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP 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 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 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: 30.0000 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 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: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.185189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.141333 restraints weight = 61797.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136301 restraints weight = 93875.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130303 restraints weight = 72885.955| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3868 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= 0.130 Angle : 0.558 12.465 42200 Z= 0.284 Chirality : 0.044 0.242 4878 Planarity : 0.004 0.054 5347 Dihedral : 5.266 56.708 4990 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 1.80 % Allowed : 11.34 % Favored : 86.86 % 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: 667 sheet: 0.56 (0.17), residues: 961 loop : -1.04 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.004 0.001 HIS C 519 PHE 0.020 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 0.00327 ( 29) link_NAG-ASN : angle 2.58134 ( 87) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.21159 ( 45) hydrogen bonds : bond 0.04656 ( 1118) hydrogen bonds : angle 5.22229 ( 3225) SS BOND : bond 0.00322 ( 51) SS BOND : angle 1.29340 ( 102) covalent geometry : bond 0.00298 (30840) covalent geometry : angle 0.54195 (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 268 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 3.416 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: 0.9087 (tt) cc_final: 0.8814 (mt) REVERT: B 164 ASN cc_start: 0.3993 (m-40) cc_final: 0.3725 (t0) REVERT: B 584 ILE cc_start: 0.8238 (mm) cc_final: 0.7967 (tt) REVERT: B 902 MET cc_start: 0.8586 (mmm) cc_final: 0.8326 (tpt) REVERT: B 1029 MET cc_start: 0.8715 (tpp) cc_final: 0.8396 (ttm) REVERT: C 207 HIS cc_start: 0.6772 (t-170) cc_final: 0.6544 (t70) REVERT: C 1031 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: E 34 MET cc_start: 0.1849 (mmp) cc_final: 0.0407 (tpp) REVERT: E 35 CYS cc_start: -0.0028 (OUTLIER) cc_final: -0.1162 (p) REVERT: F 4 MET cc_start: 0.0725 (mpp) cc_final: 0.0080 (ttm) REVERT: H 4 MET cc_start: 0.5121 (ptm) cc_final: 0.4889 (ptm) outliers start: 59 outliers final: 38 residues processed: 252 average time/residue: 0.3691 time to fit residues: 158.9013 Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP 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 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 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 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 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 961 THR 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: 6.9990 chunk 259 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 340 optimal weight: 40.0000 chunk 158 optimal weight: 0.3980 chunk 357 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 263 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 B 901 GLN C 207 HIS C 901 GLN C1005 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.193639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.169195 restraints weight = 67759.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.167804 restraints weight = 110037.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.165464 restraints weight = 105810.697| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30935 Z= 0.197 Angle : 0.613 9.857 42200 Z= 0.313 Chirality : 0.046 0.247 4878 Planarity : 0.004 0.053 5347 Dihedral : 5.242 57.544 4990 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 1.98 % Allowed : 12.63 % Favored : 85.39 % 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: -0.17 (0.14), residues: 3737 helix: 1.89 (0.21), residues: 678 sheet: 0.48 (0.16), residues: 999 loop : -1.15 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 104 HIS 0.007 0.001 HIS B 519 PHE 0.040 0.002 PHE E 69 TYR 0.024 0.001 TYR A1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 29) link_NAG-ASN : angle 2.74295 ( 87) link_BETA1-4 : bond 0.00268 ( 15) link_BETA1-4 : angle 1.35315 ( 45) hydrogen bonds : bond 0.05538 ( 1118) hydrogen bonds : angle 5.33918 ( 3225) SS BOND : bond 0.00737 ( 51) SS BOND : angle 1.52517 ( 102) covalent geometry : bond 0.00467 (30840) covalent geometry : angle 0.59592 (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 263 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7216 (tp40) REVERT: B 584 ILE cc_start: 0.8178 (mm) cc_final: 0.7768 (tt) REVERT: B 902 MET cc_start: 0.8679 (mmm) cc_final: 0.8333 (tpt) REVERT: B 1002 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8092 (tm-30) REVERT: B 1029 MET cc_start: 0.8911 (tpp) cc_final: 0.8651 (ttm) REVERT: C 207 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5861 (t70) REVERT: E 34 MET cc_start: 0.1821 (mmp) cc_final: 0.0350 (tmm) REVERT: E 35 CYS cc_start: -0.0561 (OUTLIER) cc_final: -0.0872 (p) REVERT: E 83 MET cc_start: 0.1581 (tpp) cc_final: -0.0109 (ptp) REVERT: I 34 MET cc_start: 0.2366 (tmm) cc_final: 0.1974 (ttt) outliers start: 65 outliers final: 47 residues processed: 252 average time/residue: 0.3620 time to fit residues: 156.3782 Evaluate side-chains 220 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 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 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 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 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 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 915 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 239 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 206 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 66 HIS B 755 GLN C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.183138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132325 restraints weight = 61384.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128342 restraints weight = 69231.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120592 restraints weight = 46060.179| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30935 Z= 0.124 Angle : 0.555 9.610 42200 Z= 0.282 Chirality : 0.044 0.235 4878 Planarity : 0.004 0.051 5347 Dihedral : 4.990 56.965 4990 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 1.83 % Allowed : 13.33 % Favored : 84.84 % 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: 2.13 (0.21), residues: 679 sheet: 0.56 (0.16), residues: 999 loop : -1.11 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS C 207 PHE 0.019 0.001 PHE C 541 TYR 0.023 0.001 TYR B1067 ARG 0.007 0.000 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 29) link_NAG-ASN : angle 2.49246 ( 87) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.21627 ( 45) hydrogen bonds : bond 0.04748 ( 1118) hydrogen bonds : angle 5.13238 ( 3225) SS BOND : bond 0.00356 ( 51) SS BOND : angle 1.38696 ( 102) covalent geometry : bond 0.00286 (30840) covalent geometry : angle 0.53944 (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 245 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 3.339 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: 0.9082 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 584 ILE cc_start: 0.8363 (mm) cc_final: 0.7814 (tt) REVERT: B 902 MET cc_start: 0.8543 (mmm) cc_final: 0.8338 (tpt) REVERT: B 1029 MET cc_start: 0.8749 (tpp) cc_final: 0.8483 (ttm) REVERT: C 207 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6438 (t70) REVERT: E 34 MET cc_start: 0.1960 (mmp) cc_final: 0.0004 (tmm) REVERT: E 35 CYS cc_start: 0.0187 (OUTLIER) cc_final: -0.1134 (p) REVERT: E 83 MET cc_start: 0.1775 (tpp) cc_final: 0.0282 (ptm) REVERT: F 4 MET cc_start: 0.1957 (ttm) cc_final: 0.0509 (mpp) REVERT: I 34 MET cc_start: 0.3868 (tmm) cc_final: 0.3242 (ttt) outliers start: 60 outliers final: 44 residues processed: 232 average time/residue: 0.3481 time to fit residues: 140.3684 Evaluate side-chains 213 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 749 CYS 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 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1115 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 220 PHE 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 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 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 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 H residue 4 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 149 optimal weight: 7.9990 chunk 240 optimal weight: 30.0000 chunk 303 optimal weight: 0.7980 chunk 367 optimal weight: 0.0170 chunk 349 optimal weight: 20.0000 chunk 174 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 318 optimal weight: 0.5980 chunk 265 optimal weight: 3.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 C 901 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.195552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.170312 restraints weight = 68130.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.169726 restraints weight = 114166.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.168195 restraints weight = 103792.453| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30935 Z= 0.109 Angle : 0.545 9.535 42200 Z= 0.274 Chirality : 0.044 0.368 4878 Planarity : 0.004 0.049 5347 Dihedral : 4.795 56.521 4990 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.86 % Allowed : 13.72 % Favored : 84.42 % 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: 0.08 (0.14), residues: 3737 helix: 2.23 (0.21), residues: 678 sheet: 0.69 (0.17), residues: 964 loop : -1.05 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.024 0.001 HIS C 207 PHE 0.023 0.001 PHE A 133 TYR 0.029 0.001 TYR B 170 ARG 0.002 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 29) link_NAG-ASN : angle 2.53327 ( 87) link_BETA1-4 : bond 0.00370 ( 15) link_BETA1-4 : angle 1.15303 ( 45) hydrogen bonds : bond 0.04403 ( 1118) hydrogen bonds : angle 4.98947 ( 3225) SS BOND : bond 0.00334 ( 51) SS BOND : angle 1.23631 ( 102) covalent geometry : bond 0.00245 (30840) covalent geometry : angle 0.52984 (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 252 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 3.549 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: 0.9065 (OUTLIER) cc_final: 0.8825 (mt) REVERT: B 584 ILE cc_start: 0.8224 (mm) cc_final: 0.7796 (tt) REVERT: B 902 MET cc_start: 0.8645 (mmm) cc_final: 0.8370 (tpt) REVERT: B 1029 MET cc_start: 0.8687 (tpp) cc_final: 0.8455 (ttm) REVERT: C 41 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7791 (tppt) REVERT: C 207 HIS cc_start: 0.6182 (OUTLIER) cc_final: 0.5862 (t70) REVERT: E 34 MET cc_start: 0.1847 (mmp) cc_final: 0.0101 (tmm) REVERT: E 83 MET cc_start: 0.1945 (tpp) cc_final: -0.0243 (ptp) REVERT: F 4 MET cc_start: 0.1491 (ttm) cc_final: -0.0028 (mpp) REVERT: H 47 LEU cc_start: 0.1694 (OUTLIER) cc_final: 0.1380 (mt) REVERT: I 34 MET cc_start: 0.2328 (tmm) cc_final: 0.2007 (ttt) outliers start: 61 outliers final: 44 residues processed: 237 average time/residue: 0.3823 time to fit residues: 156.9796 Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 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 749 CYS 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 934 ILE Chi-restraints excluded: chain A residue 938 LEU 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 31 SER 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 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 963 VAL Chi-restraints excluded: chain C residue 980 ILE 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 G residue 120 VAL Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 67 optimal weight: 0.6980 chunk 341 optimal weight: 40.0000 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 214 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 355 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 B 901 GLN C 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.195030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.170963 restraints weight = 68184.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.169776 restraints weight = 114571.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.167515 restraints weight = 104361.416| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30935 Z= 0.112 Angle : 0.560 16.072 42200 Z= 0.280 Chirality : 0.044 0.219 4878 Planarity : 0.004 0.049 5347 Dihedral : 4.702 56.464 4990 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 1.62 % Allowed : 14.24 % 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: 0.11 (0.14), residues: 3737 helix: 2.27 (0.21), residues: 673 sheet: 0.71 (0.17), residues: 964 loop : -1.02 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.011 0.001 HIS C 207 PHE 0.022 0.001 PHE A 106 TYR 0.021 0.001 TYR B1067 ARG 0.002 0.000 ARG A 646 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 29) link_NAG-ASN : angle 2.37043 ( 87) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.11294 ( 45) hydrogen bonds : bond 0.04288 ( 1118) hydrogen bonds : angle 4.93774 ( 3225) SS BOND : bond 0.00358 ( 51) SS BOND : angle 1.33391 ( 102) covalent geometry : bond 0.00252 (30840) covalent geometry : angle 0.54617 (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 233 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 3.583 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 779 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7848 (tm-30) REVERT: A 1115 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8875 (mt) REVERT: B 902 MET cc_start: 0.8663 (mmm) cc_final: 0.8400 (tpt) REVERT: B 1029 MET cc_start: 0.8679 (tpp) cc_final: 0.8439 (ttm) REVERT: C 41 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7861 (tppt) REVERT: C 207 HIS cc_start: 0.6107 (OUTLIER) cc_final: 0.5585 (t70) REVERT: E 34 MET cc_start: 0.1749 (mmp) cc_final: 0.0181 (tpp) REVERT: E 83 MET cc_start: 0.1932 (tpp) cc_final: -0.0382 (ptp) REVERT: F 4 MET cc_start: 0.1456 (ttm) cc_final: 0.0090 (mpp) REVERT: H 47 LEU cc_start: 0.1652 (OUTLIER) cc_final: 0.1355 (mt) REVERT: I 34 MET cc_start: 0.2414 (tmm) cc_final: 0.2204 (ttt) outliers start: 53 outliers final: 46 residues processed: 219 average time/residue: 0.3719 time to fit residues: 142.0448 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 : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 742 ILE 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 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 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 31 SER 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 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 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 G residue 120 VAL Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 47 LEU 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: 20.0000 chunk 139 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 chunk 368 optimal weight: 40.0000 chunk 247 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 804 GLN A 926 GLN A 965 GLN A1088 HIS B 66 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 901 GLN C1088 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 42 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.183576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.158726 restraints weight = 66792.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.156809 restraints weight = 117245.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155490 restraints weight = 106458.324| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.128 30935 Z= 0.699 Angle : 1.169 14.702 42200 Z= 0.598 Chirality : 0.067 0.422 4878 Planarity : 0.007 0.079 5347 Dihedral : 7.541 59.207 4990 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.87 % Favored : 92.11 % Rotamer: Outliers : 2.47 % Allowed : 14.30 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.59 (0.13), residues: 3737 helix: -0.14 (0.19), residues: 702 sheet: -0.15 (0.17), residues: 878 loop : -1.83 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP A 64 HIS 0.033 0.004 HIS C 207 PHE 0.048 0.005 PHE C 906 TYR 0.045 0.004 TYR A1067 ARG 0.017 0.002 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.01035 ( 29) link_NAG-ASN : angle 4.50501 ( 87) link_BETA1-4 : bond 0.00563 ( 15) link_BETA1-4 : angle 2.70924 ( 45) hydrogen bonds : bond 0.09881 ( 1118) hydrogen bonds : angle 6.68045 ( 3225) SS BOND : bond 0.00774 ( 51) SS BOND : angle 2.95539 ( 102) covalent geometry : bond 0.01687 (30840) covalent geometry : angle 1.14168 (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 266 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 185 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8909 (mp) REVERT: B 902 MET cc_start: 0.8788 (mmm) cc_final: 0.8423 (tpt) REVERT: C 200 TYR cc_start: 0.6382 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: C 823 PHE cc_start: 0.8386 (t80) cc_final: 0.8117 (t80) REVERT: C 987 PRO cc_start: 0.8325 (Cg_exo) cc_final: 0.7865 (Cg_endo) REVERT: C 988 GLU cc_start: 0.7369 (mp0) cc_final: 0.7007 (mp0) REVERT: E 34 MET cc_start: 0.2108 (mmp) cc_final: 0.0403 (tpp) REVERT: E 79 VAL cc_start: -0.3911 (OUTLIER) cc_final: -0.4372 (m) REVERT: E 83 MET cc_start: 0.2648 (tpp) cc_final: -0.0602 (ptp) REVERT: F 4 MET cc_start: 0.1705 (ttm) cc_final: 0.0277 (mpp) REVERT: H 47 LEU cc_start: 0.1942 (OUTLIER) cc_final: 0.1586 (mt) outliers start: 81 outliers final: 57 residues processed: 256 average time/residue: 0.3629 time to fit residues: 161.4701 Evaluate side-chains 197 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 157 PHE 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 574 ASP Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 660 TYR 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 778 THR 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 934 ILE Chi-restraints excluded: chain A residue 938 LEU 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 240 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 651 ILE 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 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 240 THR 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 555 SER 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 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 G residue 120 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: 0.9980 chunk 345 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 256 optimal weight: 2.9990 chunk 292 optimal weight: 0.9980 chunk 327 optimal weight: 40.0000 chunk 334 optimal weight: 20.0000 chunk 70 optimal weight: 0.0770 chunk 351 optimal weight: 8.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 978 ASN B 66 HIS C 188 ASN C 207 HIS ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.190815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.166005 restraints weight = 66865.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.165241 restraints weight = 114887.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.163912 restraints weight = 109103.777| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30935 Z= 0.144 Angle : 0.668 16.117 42200 Z= 0.337 Chirality : 0.047 0.462 4878 Planarity : 0.005 0.065 5347 Dihedral : 6.017 59.431 4990 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 1.49 % Allowed : 16.01 % 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: -0.76 (0.13), residues: 3737 helix: 1.29 (0.20), residues: 698 sheet: 0.15 (0.17), residues: 923 loop : -1.49 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.006 0.001 HIS C 207 PHE 0.022 0.002 PHE B 168 TYR 0.025 0.001 TYR B1067 ARG 0.005 0.001 ARG G 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 29) link_NAG-ASN : angle 3.32463 ( 87) link_BETA1-4 : bond 0.00506 ( 15) link_BETA1-4 : angle 1.70823 ( 45) hydrogen bonds : bond 0.05749 ( 1118) hydrogen bonds : angle 5.52172 ( 3225) SS BOND : bond 0.00424 ( 51) SS BOND : angle 1.44193 ( 102) covalent geometry : bond 0.00316 (30840) covalent geometry : angle 0.64647 (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 220 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: B 902 MET cc_start: 0.8686 (mmm) cc_final: 0.8330 (tpt) REVERT: B 1002 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 41 LYS cc_start: 0.8173 (mmmm) cc_final: 0.7843 (mmmm) REVERT: C 190 ARG cc_start: 0.5016 (mpt180) cc_final: 0.4607 (mmt90) REVERT: C 823 PHE cc_start: 0.8097 (t80) cc_final: 0.7843 (t80) REVERT: E 34 MET cc_start: 0.1769 (mmp) cc_final: 0.0036 (tpt) REVERT: E 79 VAL cc_start: -0.4293 (OUTLIER) cc_final: -0.4721 (m) REVERT: E 83 MET cc_start: 0.2202 (tpp) cc_final: -0.0730 (ptp) REVERT: F 4 MET cc_start: 0.1427 (ttm) cc_final: 0.0560 (mpp) REVERT: H 47 LEU cc_start: 0.1812 (OUTLIER) cc_final: 0.1521 (mt) outliers start: 49 outliers final: 37 residues processed: 206 average time/residue: 0.3563 time to fit residues: 126.2836 Evaluate side-chains 196 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR 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 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 1129 VAL Chi-restraints excluded: chain B residue 42 VAL 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 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 133 PHE 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 991 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 120 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 157 optimal weight: 0.9990 chunk 371 optimal weight: 9.9990 chunk 202 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.190044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.164915 restraints weight = 67133.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.163992 restraints weight = 119175.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.162868 restraints weight = 109573.926| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30935 Z= 0.171 Angle : 0.636 15.962 42200 Z= 0.320 Chirality : 0.046 0.365 4878 Planarity : 0.004 0.056 5347 Dihedral : 5.675 57.790 4990 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.32 % Rotamer: Outliers : 1.31 % Allowed : 16.50 % Favored : 82.19 % 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: -0.61 (0.13), residues: 3737 helix: 1.44 (0.20), residues: 703 sheet: 0.24 (0.17), residues: 922 loop : -1.40 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.006 0.001 HIS B 66 PHE 0.020 0.002 PHE A 970 TYR 0.024 0.001 TYR B1067 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 29) link_NAG-ASN : angle 2.96874 ( 87) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.49681 ( 45) hydrogen bonds : bond 0.05582 ( 1118) hydrogen bonds : angle 5.32661 ( 3225) SS BOND : bond 0.00400 ( 51) SS BOND : angle 1.47491 ( 102) covalent geometry : bond 0.00409 (30840) covalent geometry : angle 0.61727 (41966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9846.70 seconds wall clock time: 174 minutes 9.57 seconds (10449.57 seconds total)