Starting phenix.real_space_refine on Mon Aug 25 19:52:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8itu_35328/08_2025/8itu_35328_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8itu_35328/08_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_35328/08_2025/8itu_35328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8itu_35328/08_2025/8itu_35328.map" model { file = "/net/cci-nas-00/data/ceres_data/8itu_35328/08_2025/8itu_35328_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8itu_35328/08_2025/8itu_35328_neut.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 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: 5.81, per 1000 atoms: 0.19 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: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.36 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: 6.74 Time building geometry restraints manager: 2.97 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 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 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 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: 12.210 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: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.510 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- 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 : 9.41 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG H 61 TYR 0.014 0.001 TYR C 396 PHE 0.035 0.001 PHE A 906 TRP 0.028 0.001 TRP E 112 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00386 (30840) covalent geometry : angle 0.57720 (41966) SS BOND : bond 0.00271 ( 51) SS BOND : angle 0.86243 ( 102) hydrogen bonds : bond 0.21036 ( 1118) hydrogen bonds : angle 8.29760 ( 3225) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.01541 ( 45) link_NAG-ASN : bond 0.00498 ( 29) link_NAG-ASN : angle 4.29089 ( 87) *********************** 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 : 1.299 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: symmetry clash REVERT: A 104 TRP cc_start: 0.6920 (m-90) cc_final: 0.6675 (m-90) REVERT: A 200 TYR cc_start: 0.7798 (m-10) cc_final: 0.7586 (m-80) REVERT: A 270 LEU cc_start: 0.8634 (mt) cc_final: 0.8400 (mp) REVERT: A 309 GLU cc_start: 0.7559 (mp0) cc_final: 0.7265 (mp0) REVERT: A 546 LEU cc_start: 0.6144 (tt) cc_final: 0.5908 (pp) REVERT: A 574 ASP cc_start: 0.7144 (t70) cc_final: 0.6451 (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: 0.8150 (tp) REVERT: A 1041 ASP cc_start: 0.7829 (m-30) cc_final: 0.7570 (t0) REVERT: B 128 ILE cc_start: 0.8582 (mp) cc_final: 0.8375 (mm) REVERT: B 140 PHE cc_start: 0.6479 (p90) cc_final: 0.6005 (p90) REVERT: B 186 PHE cc_start: 0.7039 (m-80) cc_final: 0.6439 (p90) REVERT: B 206 LYS cc_start: 0.7166 (tppt) cc_final: 0.6656 (mmtt) REVERT: B 228 ASP cc_start: 0.7188 (t0) cc_final: 0.6965 (t0) REVERT: B 314 GLN cc_start: 0.8284 (tt0) cc_final: 0.8036 (tt0) REVERT: B 796 TYR cc_start: 0.6630 (t80) cc_final: 0.6163 (t80) REVERT: B 950 ASP cc_start: 0.8111 (m-30) cc_final: 0.7672 (m-30) REVERT: B 1050 MET cc_start: 0.7923 (ptt) cc_final: 0.7645 (ptt) REVERT: C 140 PHE cc_start: 0.7531 (p90) cc_final: 0.6636 (p90) REVERT: C 153 MET cc_start: 0.4193 (tmm) cc_final: 0.2961 (pmm) REVERT: C 950 ASP cc_start: 0.8045 (m-30) cc_final: 0.7824 (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: 0.8422 (p) REVERT: D 4 MET cc_start: 0.0939 (ptp) cc_final: 0.0601 (ptp) REVERT: E 34 MET cc_start: 0.2500 (mmp) cc_final: 0.0855 (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: 0.5208 (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: 0.3959 (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: 0.1867 time to fit residues: 156.7048 Evaluate side-chains 265 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 188 ASN A 536 ASN A 901 GLN A 926 GLN A1002 GLN B 66 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 919 ASN C 125 ASN C 207 HIS C 354 ASN C 804 GLN C 935 GLN H 37 GLN H 38 GLN H 70 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.196422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.171637 restraints weight = 68795.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.171138 restraints weight = 127243.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.171074 restraints weight = 111388.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.169919 restraints weight = 105858.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.169790 restraints weight = 109412.050| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 30935 Z= 0.264 Angle : 0.759 12.494 42200 Z= 0.391 Chirality : 0.050 0.333 4878 Planarity : 0.006 0.069 5347 Dihedral : 6.472 59.426 4990 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 1.74 % Allowed : 8.36 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.13), residues: 3737 helix: 1.38 (0.20), residues: 680 sheet: 0.34 (0.17), residues: 959 loop : -1.18 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 237 TYR 0.038 0.002 TYR B1067 PHE 0.036 0.002 PHE A 906 TRP 0.016 0.002 TRP A 436 HIS 0.009 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00618 (30840) covalent geometry : angle 0.73635 (41966) SS BOND : bond 0.01790 ( 51) SS BOND : angle 1.86183 ( 102) hydrogen bonds : bond 0.06447 ( 1118) hydrogen bonds : angle 6.12526 ( 3225) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.58375 ( 45) link_NAG-ASN : bond 0.00749 ( 29) link_NAG-ASN : angle 3.51595 ( 87) *********************** 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 325 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.096 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: symmetry clash REVERT: A 239 GLN cc_start: 0.7171 (tp-100) cc_final: 0.6832 (tp40) REVERT: A 697 MET cc_start: 0.8408 (ptm) cc_final: 0.8099 (ptt) REVERT: A 1041 ASP cc_start: 0.7977 (m-30) cc_final: 0.7709 (t0) REVERT: B 314 GLN cc_start: 0.7972 (tt0) cc_final: 0.7758 (tt0) REVERT: B 589 PRO cc_start: 0.5812 (Cg_exo) cc_final: 0.5607 (Cg_endo) REVERT: B 902 MET cc_start: 0.8628 (mmm) cc_final: 0.8402 (tpt) REVERT: C 207 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.5828 (t70) REVERT: C 977 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8852 (mp) REVERT: E 34 MET cc_start: 0.1923 (mmp) cc_final: 0.0532 (tpp) REVERT: F 4 MET cc_start: 0.0942 (ptp) cc_final: 0.0739 (mpp) outliers start: 57 outliers final: 36 residues processed: 314 average time/residue: 0.1664 time to fit residues: 87.9404 Evaluate side-chains 227 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 615 VAL 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 778 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 617 CYS 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 207 HIS 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 780 GLU 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 977 LEU 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 133 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 347 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 926 GLN A1010 GLN B 66 HIS B 188 ASN B 207 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C1005 GLN C1010 GLN D 38 GLN H 31 ASN H 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.197381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.173689 restraints weight = 68937.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.172725 restraints weight = 117506.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.171295 restraints weight = 102500.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.170755 restraints weight = 98507.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.169626 restraints weight = 103826.607| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30935 Z= 0.133 Angle : 0.587 12.115 42200 Z= 0.297 Chirality : 0.045 0.278 4878 Planarity : 0.004 0.058 5347 Dihedral : 5.776 56.724 4990 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 1.71 % Allowed : 10.73 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3737 helix: 2.14 (0.21), residues: 670 sheet: 0.50 (0.17), residues: 964 loop : -1.10 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 98 TYR 0.022 0.001 TYR A1067 PHE 0.022 0.001 PHE A 133 TRP 0.011 0.001 TRP A 104 HIS 0.021 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00299 (30840) covalent geometry : angle 0.56701 (41966) SS BOND : bond 0.00582 ( 51) SS BOND : angle 1.53667 ( 102) hydrogen bonds : bond 0.05085 ( 1118) hydrogen bonds : angle 5.53583 ( 3225) link_BETA1-4 : bond 0.00433 ( 15) link_BETA1-4 : angle 1.27099 ( 45) link_NAG-ASN : bond 0.00385 ( 29) link_NAG-ASN : angle 2.90021 ( 87) *********************** 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 269 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.014 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: A 239 GLN cc_start: 0.7291 (tp-100) cc_final: 0.7040 (tp40) REVERT: A 697 MET cc_start: 0.8393 (ptm) cc_final: 0.8190 (ptp) REVERT: A 779 GLN cc_start: 0.8109 (tp40) cc_final: 0.7878 (tp40) REVERT: B 725 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 133 PHE cc_start: 0.5118 (m-80) cc_final: 0.4913 (t80) REVERT: C 207 HIS cc_start: 0.6065 (OUTLIER) cc_final: 0.5647 (t-90) REVERT: E 34 MET cc_start: 0.1937 (mmp) cc_final: 0.0950 (tpp) REVERT: H 4 MET cc_start: 0.4139 (OUTLIER) cc_final: 0.3939 (ptm) REVERT: I 34 MET cc_start: 0.2243 (tmm) cc_final: 0.1955 (ttt) outliers start: 56 outliers final: 34 residues processed: 252 average time/residue: 0.1714 time to fit residues: 73.4162 Evaluate side-chains 220 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR 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 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 307 THR 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 62 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 394 ASN 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 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain I residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 139 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 249 optimal weight: 0.0470 chunk 347 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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 115 GLN C 207 HIS H 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.196233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.171237 restraints weight = 67998.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.169886 restraints weight = 125009.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.169269 restraints weight = 112421.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.168651 restraints weight = 103210.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.167925 restraints weight = 107012.846| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.4061 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= 0.133 Angle : 0.565 10.638 42200 Z= 0.287 Chirality : 0.044 0.249 4878 Planarity : 0.004 0.056 5347 Dihedral : 5.387 56.885 4990 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.98 % Allowed : 11.62 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3737 helix: 2.13 (0.21), residues: 667 sheet: 0.48 (0.17), residues: 973 loop : -1.12 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.023 0.001 TYR B1067 PHE 0.018 0.001 PHE C 329 TRP 0.012 0.001 TRP A 104 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00307 (30840) covalent geometry : angle 0.54751 (41966) SS BOND : bond 0.00430 ( 51) SS BOND : angle 1.38840 ( 102) hydrogen bonds : bond 0.04859 ( 1118) hydrogen bonds : angle 5.33129 ( 3225) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.25620 ( 45) link_NAG-ASN : bond 0.00329 ( 29) link_NAG-ASN : angle 2.65600 ( 87) *********************** 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 262 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 779 GLN cc_start: 0.8129 (tp40) cc_final: 0.7850 (tp40) REVERT: A 854 LYS cc_start: 0.5760 (tptt) cc_final: 0.5203 (tptt) REVERT: C 207 HIS cc_start: 0.6176 (OUTLIER) cc_final: 0.5808 (t-90) REVERT: E 34 MET cc_start: 0.1843 (mmp) cc_final: 0.0568 (tpp) REVERT: E 35 CYS cc_start: -0.0487 (OUTLIER) cc_final: -0.0958 (p) REVERT: F 4 MET cc_start: 0.0401 (mpp) cc_final: -0.0438 (ttp) REVERT: H 4 MET cc_start: 0.4240 (ptm) cc_final: 0.4022 (ptm) REVERT: I 34 MET cc_start: 0.2549 (tmm) cc_final: 0.2248 (ttt) outliers start: 65 outliers final: 42 residues processed: 249 average time/residue: 0.1643 time to fit residues: 70.5243 Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 240 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 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 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 158 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 202 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 271 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 349 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS C 207 HIS C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.183441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137735 restraints weight = 61417.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132303 restraints weight = 92860.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126873 restraints weight = 72825.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125422 restraints weight = 66457.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.126061 restraints weight = 63685.582| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30935 Z= 0.145 Angle : 0.566 10.871 42200 Z= 0.286 Chirality : 0.044 0.237 4878 Planarity : 0.004 0.053 5347 Dihedral : 5.146 56.924 4990 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.86 % Allowed : 12.47 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3737 helix: 2.06 (0.21), residues: 679 sheet: 0.52 (0.17), residues: 965 loop : -1.13 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 98 TYR 0.022 0.001 TYR B1067 PHE 0.026 0.001 PHE A 133 TRP 0.014 0.001 TRP A 104 HIS 0.023 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00340 (30840) covalent geometry : angle 0.54947 (41966) SS BOND : bond 0.00579 ( 51) SS BOND : angle 1.32766 ( 102) hydrogen bonds : bond 0.04913 ( 1118) hydrogen bonds : angle 5.22728 ( 3225) link_BETA1-4 : bond 0.00331 ( 15) link_BETA1-4 : angle 1.25133 ( 45) link_NAG-ASN : bond 0.00325 ( 29) link_NAG-ASN : angle 2.57907 ( 87) *********************** 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 248 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 1.129 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: 0.8133 (tp40) cc_final: 0.7908 (tp40) REVERT: C 133 PHE cc_start: 0.6334 (m-80) cc_final: 0.5680 (t80) REVERT: C 207 HIS cc_start: 0.6604 (OUTLIER) cc_final: 0.6125 (t70) REVERT: E 34 MET cc_start: 0.1993 (mmp) cc_final: 0.0220 (mmm) REVERT: E 35 CYS cc_start: -0.0032 (OUTLIER) cc_final: -0.1126 (p) REVERT: E 83 MET cc_start: 0.2129 (tpp) cc_final: -0.0084 (ptp) REVERT: F 4 MET cc_start: 0.0624 (mpp) cc_final: -0.0305 (ttp) REVERT: I 34 MET cc_start: 0.3665 (tmm) cc_final: 0.3261 (ttt) outliers start: 61 outliers final: 48 residues processed: 238 average time/residue: 0.1597 time to fit residues: 66.1011 Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL 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 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR 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 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 980 ILE Chi-restraints excluded: chain A residue 1072 GLU 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 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 29 THR 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 394 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 104 optimal weight: 0.0000 chunk 115 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 271 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 197 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.4424 r_free = 0.4424 target = 0.181726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130059 restraints weight = 60556.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123426 restraints weight = 63921.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115013 restraints weight = 43337.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114746 restraints weight = 42646.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115506 restraints weight = 41452.335| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30935 Z= 0.178 Angle : 0.594 13.093 42200 Z= 0.301 Chirality : 0.045 0.235 4878 Planarity : 0.004 0.052 5347 Dihedral : 5.141 57.511 4990 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 2.38 % Allowed : 12.99 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 3737 helix: 1.89 (0.21), residues: 680 sheet: 0.53 (0.16), residues: 986 loop : -1.20 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 98 TYR 0.022 0.001 TYR B1067 PHE 0.018 0.002 PHE C 559 TRP 0.013 0.001 TRP A 104 HIS 0.038 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00425 (30840) covalent geometry : angle 0.57533 (41966) SS BOND : bond 0.00397 ( 51) SS BOND : angle 1.65698 ( 102) hydrogen bonds : bond 0.05372 ( 1118) hydrogen bonds : angle 5.25161 ( 3225) link_BETA1-4 : bond 0.00287 ( 15) link_BETA1-4 : angle 1.33601 ( 45) link_NAG-ASN : bond 0.00332 ( 29) link_NAG-ASN : angle 2.66258 ( 87) *********************** 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 256 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 178 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 HIS cc_start: 0.6791 (OUTLIER) cc_final: 0.6056 (t-90) REVERT: B 306 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8345 (t80) REVERT: C 133 PHE cc_start: 0.6934 (m-80) cc_final: 0.6037 (t80) REVERT: C 141 LEU cc_start: 0.7817 (tp) cc_final: 0.7430 (tp) REVERT: C 190 ARG cc_start: 0.5821 (mpt90) cc_final: 0.5419 (mmp80) REVERT: E 34 MET cc_start: 0.2130 (mmp) cc_final: 0.0111 (tmm) REVERT: E 35 CYS cc_start: 0.0365 (OUTLIER) cc_final: -0.1062 (p) REVERT: E 83 MET cc_start: 0.1918 (tpp) cc_final: -0.0135 (ptp) REVERT: F 4 MET cc_start: 0.0642 (mpp) cc_final: -0.0191 (ttm) REVERT: H 47 LEU cc_start: 0.2412 (OUTLIER) cc_final: 0.2203 (mt) REVERT: I 34 MET cc_start: 0.4130 (tmm) cc_final: 0.3701 (ttt) outliers start: 78 outliers final: 58 residues processed: 242 average time/residue: 0.1564 time to fit residues: 65.0894 Evaluate side-chains 224 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 162 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 327 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR 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 742 ILE 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 957 GLN Chi-restraints excluded: chain A residue 1072 GLU 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 207 HIS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 205 SER 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 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 780 GLU 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 961 THR 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 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 50 optimal weight: 8.9990 chunk 246 optimal weight: 30.0000 chunk 145 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 202 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4550 r_free = 0.4550 target = 0.194625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.169716 restraints weight = 67995.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.168259 restraints weight = 110442.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.166300 restraints weight = 101332.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.165252 restraints weight = 103793.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.164428 restraints weight = 97734.121| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30935 Z= 0.112 Angle : 0.554 15.253 42200 Z= 0.277 Chirality : 0.044 0.339 4878 Planarity : 0.004 0.050 5347 Dihedral : 4.910 56.977 4990 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 1.68 % Allowed : 14.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.14), residues: 3737 helix: 2.13 (0.21), residues: 679 sheet: 0.55 (0.16), residues: 977 loop : -1.11 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.022 0.001 TYR B1067 PHE 0.028 0.001 PHE A 133 TRP 0.015 0.001 TRP A 104 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00255 (30840) covalent geometry : angle 0.53668 (41966) SS BOND : bond 0.00310 ( 51) SS BOND : angle 1.36613 ( 102) hydrogen bonds : bond 0.04622 ( 1118) hydrogen bonds : angle 5.01838 ( 3225) link_BETA1-4 : bond 0.00403 ( 15) link_BETA1-4 : angle 1.19364 ( 45) link_NAG-ASN : bond 0.00311 ( 29) link_NAG-ASN : angle 2.61472 ( 87) *********************** 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 231 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 750 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7745 (m) REVERT: B 306 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8373 (t80) REVERT: E 34 MET cc_start: 0.2002 (mmp) cc_final: 0.0263 (tmm) REVERT: E 35 CYS cc_start: -0.0516 (OUTLIER) cc_final: -0.0721 (p) REVERT: E 83 MET cc_start: 0.1606 (tpp) cc_final: -0.0837 (mmt) outliers start: 55 outliers final: 44 residues processed: 219 average time/residue: 0.1534 time to fit residues: 58.0151 Evaluate side-chains 208 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE 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 957 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 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 306 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 826 VAL 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 62 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 582 LEU 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 826 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 35 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain H residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 262 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 159 optimal weight: 0.0270 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 965 GLN B 66 HIS C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.194706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.169789 restraints weight = 68407.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.168817 restraints weight = 115531.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.167204 restraints weight = 102730.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.166382 restraints weight = 96213.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.165542 restraints weight = 99950.686| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30935 Z= 0.112 Angle : 0.552 15.403 42200 Z= 0.277 Chirality : 0.044 0.219 4878 Planarity : 0.004 0.049 5347 Dihedral : 4.760 56.642 4990 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 1.83 % Allowed : 14.33 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.14), residues: 3737 helix: 2.17 (0.21), residues: 681 sheet: 0.57 (0.16), residues: 973 loop : -1.06 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 102 TYR 0.033 0.001 TYR B 170 PHE 0.016 0.001 PHE C 559 TRP 0.016 0.001 TRP A 104 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00256 (30840) covalent geometry : angle 0.53798 (41966) SS BOND : bond 0.00309 ( 51) SS BOND : angle 1.27236 ( 102) hydrogen bonds : bond 0.04421 ( 1118) hydrogen bonds : angle 4.91454 ( 3225) link_BETA1-4 : bond 0.00386 ( 15) link_BETA1-4 : angle 1.13679 ( 45) link_NAG-ASN : bond 0.00282 ( 29) link_NAG-ASN : angle 2.38638 ( 87) *********************** 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 235 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8358 (t80) REVERT: B 953 ASN cc_start: 0.8546 (m-40) cc_final: 0.8298 (m110) REVERT: E 34 MET cc_start: 0.1888 (mmp) cc_final: 0.0124 (tmm) REVERT: E 83 MET cc_start: 0.1573 (tpp) cc_final: -0.0922 (mmt) REVERT: F 4 MET cc_start: 0.0993 (ttm) cc_final: 0.0108 (mpp) REVERT: H 47 LEU cc_start: 0.1863 (OUTLIER) cc_final: 0.1596 (mt) outliers start: 60 outliers final: 44 residues processed: 222 average time/residue: 0.1575 time to fit residues: 59.9804 Evaluate side-chains 206 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 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 819 GLU 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 957 GLN Chi-restraints excluded: chain A residue 977 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 306 PHE 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 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 394 ASN 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 961 THR Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 120 VAL 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 82 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 173 optimal weight: 0.0170 chunk 285 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 154 optimal weight: 0.0370 chunk 293 optimal weight: 6.9990 chunk 197 optimal weight: 0.4980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 926 GLN A 965 GLN B 66 HIS B 901 GLN C 613 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 = 0.195421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.170728 restraints weight = 68303.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.169717 restraints weight = 116051.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.168074 restraints weight = 102470.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.167163 restraints weight = 97454.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.165887 restraints weight = 103783.565| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30935 Z= 0.102 Angle : 0.548 15.435 42200 Z= 0.275 Chirality : 0.043 0.211 4878 Planarity : 0.004 0.061 5347 Dihedral : 4.633 56.442 4990 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 1.52 % Allowed : 14.70 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3737 helix: 2.23 (0.21), residues: 685 sheet: 0.64 (0.17), residues: 956 loop : -1.01 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 646 TYR 0.021 0.001 TYR B 170 PHE 0.014 0.001 PHE B1121 TRP 0.018 0.001 TRP E 36 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00224 (30840) covalent geometry : angle 0.53555 (41966) SS BOND : bond 0.00331 ( 51) SS BOND : angle 1.22639 ( 102) hydrogen bonds : bond 0.04086 ( 1118) hydrogen bonds : angle 4.80305 ( 3225) link_BETA1-4 : bond 0.00415 ( 15) link_BETA1-4 : angle 1.06660 ( 45) link_NAG-ASN : bond 0.00282 ( 29) link_NAG-ASN : angle 2.23382 ( 87) *********************** 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 232 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1050 MET cc_start: 0.8834 (ptm) cc_final: 0.8611 (ptm) REVERT: E 34 MET cc_start: 0.1604 (mmp) cc_final: -0.0298 (tpp) REVERT: E 83 MET cc_start: 0.1409 (tpp) cc_final: -0.0919 (mmt) REVERT: F 4 MET cc_start: 0.1489 (ttm) cc_final: 0.0099 (mpp) REVERT: H 47 LEU cc_start: 0.1873 (OUTLIER) cc_final: 0.1581 (mt) outliers start: 50 outliers final: 43 residues processed: 221 average time/residue: 0.1619 time to fit residues: 62.4839 Evaluate side-chains 200 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 196 ASN 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 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 823 PHE 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 957 GLN Chi-restraints excluded: chain A residue 977 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 740 MET 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 88 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain 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 34 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 364 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 926 GLN A 965 GLN B 66 HIS B 505 HIS B 901 GLN C 544 ASN C 613 GLN C 901 GLN H 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.190552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.165921 restraints weight = 67143.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.164557 restraints weight = 107418.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162066 restraints weight = 112346.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.161156 restraints weight = 127216.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.159984 restraints weight = 112149.282| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 30935 Z= 0.244 Angle : 0.671 14.714 42200 Z= 0.341 Chirality : 0.047 0.217 4878 Planarity : 0.005 0.051 5347 Dihedral : 5.201 58.132 4990 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 1.74 % Allowed : 14.79 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.14), residues: 3737 helix: 1.46 (0.20), residues: 705 sheet: 0.50 (0.17), residues: 943 loop : -1.22 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 319 TYR 0.024 0.002 TYR B1067 PHE 0.034 0.002 PHE A 201 TRP 0.024 0.002 TRP A 64 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00591 (30840) covalent geometry : angle 0.65290 (41966) SS BOND : bond 0.00457 ( 51) SS BOND : angle 1.84557 ( 102) hydrogen bonds : bond 0.06156 ( 1118) hydrogen bonds : angle 5.30232 ( 3225) link_BETA1-4 : bond 0.00270 ( 15) link_BETA1-4 : angle 1.39702 ( 45) link_NAG-ASN : bond 0.00449 ( 29) link_NAG-ASN : angle 2.78119 ( 87) ********************** 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 217 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 965 GLN cc_start: 0.7953 (mm110) cc_final: 0.7576 (mt0) REVERT: B 306 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8273 (t80) REVERT: E 34 MET cc_start: 0.1736 (mmp) cc_final: 0.0726 (tpt) REVERT: E 79 VAL cc_start: -0.3814 (OUTLIER) cc_final: -0.4108 (m) REVERT: E 83 MET cc_start: 0.1584 (tpp) cc_final: -0.0963 (mmt) REVERT: F 4 MET cc_start: 0.1512 (ttm) cc_final: 0.0161 (mpp) REVERT: H 47 LEU cc_start: 0.1945 (OUTLIER) cc_final: 0.1613 (mt) outliers start: 57 outliers final: 46 residues processed: 209 average time/residue: 0.1411 time to fit residues: 51.3503 Evaluate side-chains 201 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP 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 289 VAL 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 602 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 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 938 LEU Chi-restraints excluded: chain A residue 977 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 306 PHE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 826 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 50 CYS 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 121 optimal weight: 0.3980 chunk 364 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 285 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 66 HIS C 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.193734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.168278 restraints weight = 68105.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.167257 restraints weight = 112936.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.166078 restraints weight = 86605.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.165727 restraints weight = 91849.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.164711 restraints weight = 90343.076| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.5585 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= 0.112 Angle : 0.563 14.871 42200 Z= 0.284 Chirality : 0.044 0.222 4878 Planarity : 0.004 0.048 5347 Dihedral : 4.845 57.164 4990 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 1.16 % Allowed : 15.43 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3737 helix: 1.95 (0.21), residues: 697 sheet: 0.56 (0.17), residues: 963 loop : -1.11 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 190 TYR 0.022 0.001 TYR B1067 PHE 0.023 0.001 PHE A 565 TRP 0.018 0.001 TRP A 104 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00251 (30840) covalent geometry : angle 0.54986 (41966) SS BOND : bond 0.00319 ( 51) SS BOND : angle 1.25584 ( 102) hydrogen bonds : bond 0.04588 ( 1118) hydrogen bonds : angle 4.94468 ( 3225) link_BETA1-4 : bond 0.00440 ( 15) link_BETA1-4 : angle 1.14840 ( 45) link_NAG-ASN : bond 0.00277 ( 29) link_NAG-ASN : angle 2.32360 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4478.73 seconds wall clock time: 78 minutes 43.61 seconds (4723.61 seconds total)