Starting phenix.real_space_refine on Mon Aug 25 19:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h01_34408/08_2025/8h01_34408.map" } resolution = 3.7 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= 0.037 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 38 residue(s): 0.02s 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: 5.56, per 1000 atoms: 0.18 Number of scatterers: 30144 At special positions: 0 Unit cell: (147.264, 162.24, 198.016, 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 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 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 69 sheets defined 20.7% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 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: 3.569A 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: 3.973A 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: 4.054A 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: 3.543A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.613A 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: 4.499A 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: 3.562A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.553A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.947A 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: 4.450A 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: 4.359A 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: 4.092A 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: 3.847A 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: 4.068A 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: 3.861A 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: 8.893A 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: 6.978A 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: 5.153A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.344A 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: 6.364A 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: 11.201A 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: 7.091A 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: 6.934A 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: 6.223A 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: 7.088A 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: 4.344A 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: 9.978A 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: 8.668A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.240A 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: 6.394A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.914A 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: 4.187A 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: 5.375A 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: 3.561A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.763A 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: 3.786A 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: 3.815A 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: 6.790A 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: 5.303A 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: 6.975A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A 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: 6.886A 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: 7.108A 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: 5.780A 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: 6.557A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.418A 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: 6.578A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.210A 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: 7.054A 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: 6.557A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.418A 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: 6.072A 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: 3.765A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.241A 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: 4.739A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.734A 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: 3.521A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.781A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AG2, 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=AG3, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.407A 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=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.590A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.522A 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=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: 7.968A 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=AG8, 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: 7.968A 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=AG9, 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=AH1, 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: 7.452A pdb=" N LYS H 110 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 6.992A 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=AH2, first strand: chain 'H' and resid 48 through 49 Processing sheet with id=AH3, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.670A 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=AH4, 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=AH5, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AH6, first strand: chain 'I' and resid 49 through 50 1189 hydrogen bonds defined for protein. 3240 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: 5.78 Time building geometry restraints manager: 3.11 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: 9492 1.34 - 1.46: 6766 1.46 - 1.58: 14405 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 -0.039 1.04e-02 9.25e+03 1.38e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.25e-02 6.40e+03 8.84e+00 bond pdb=" N LYS F 45 " pdb=" CA LYS F 45 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.21e-02 6.83e+03 7.70e+00 bond pdb=" N ASP G 33 " pdb=" CA ASP G 33 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.66e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.43e+00 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 40853 1.55 - 3.10: 977 3.10 - 4.65: 113 4.65 - 6.21: 19 6.21 - 7.76: 4 Bond angle restraints: 41966 Sorted by residual: angle pdb=" N GLY F 41 " pdb=" CA GLY F 41 " pdb=" C GLY F 41 " ideal model delta sigma weight residual 115.36 110.14 5.22 1.33e+00 5.65e-01 1.54e+01 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 112.43 108.83 3.60 9.20e-01 1.18e+00 1.53e+01 angle pdb=" N GLY A 857 " pdb=" CA GLY A 857 " pdb=" C GLY A 857 " ideal model delta sigma weight residual 115.27 110.10 5.17 1.41e+00 5.03e-01 1.35e+01 angle pdb=" CA ASN C 331 " pdb=" C ASN C 331 " pdb=" O ASN C 331 " ideal model delta sigma weight residual 122.64 118.21 4.43 1.25e+00 6.40e-01 1.26e+01 angle pdb=" CA ASN B 331 " pdb=" C ASN B 331 " pdb=" O ASN B 331 " ideal model delta sigma weight residual 122.41 118.19 4.22 1.21e+00 6.83e-01 1.22e+01 ... (remaining 41961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17253 18.00 - 35.99: 1323 35.99 - 53.99: 246 53.99 - 71.99: 51 71.99 - 89.99: 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 -10.52 -75.48 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 -25.07 -60.93 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 34.80 58.20 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 18904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 4876 0.307 - 0.613: 1 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.534: 1 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 -0.87 -1.53 2.00e-01 2.50e+01 5.88e+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 9.40e+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 1.79e+00 ... (remaining 4875 not shown) Planarity restraints: 5376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.041 2.00e-02 2.50e+03 9.43e-02 1.11e+02 pdb=" CG ASN C 331 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.169 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.104 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 5.81e-02 5.41e+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 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.000 2.00e-02 2.50e+03 1.97e-02 4.87e+00 pdb=" CG ASN B 234 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.021 2.00e-02 2.50e+03 ... (remaining 5373 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2627 2.74 - 3.28: 30316 3.28 - 3.82: 49863 3.82 - 4.36: 57334 4.36 - 4.90: 100558 Nonbonded interactions: 240698 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 2.208 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 240693 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: 10.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.330 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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= 0.190 Angle : 0.635 41.741 42200 Z= 0.323 Chirality : 0.050 1.534 4878 Planarity : 0.004 0.058 5347 Dihedral : 13.235 89.985 11676 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.08 (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 0.00376 (30840) covalent geometry : angle 0.57022 (41966) SS BOND : bond 0.00264 ( 51) SS BOND : angle 0.86275 ( 102) hydrogen bonds : bond 0.21015 ( 1120) hydrogen bonds : angle 8.30560 ( 3240) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.01355 ( 45) link_NAG-ASN : bond 0.00497 ( 29) link_NAG-ASN : angle 6.10833 ( 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 110 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.103 Fit side-chains REVERT: A 377 PHE cc_start: 0.8722 (p90) cc_final: 0.8402 (p90) REVERT: A 456 PHE cc_start: 0.8695 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1050 MET cc_start: 0.8740 (ptt) cc_final: 0.8526 (ptt) REVERT: B 1005 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8152 (tm-30) REVERT: F 43 PRO cc_start: 0.6275 (Cg_exo) cc_final: 0.6037 (Cg_endo) REVERT: H 4 MET cc_start: 0.4318 (ttm) cc_final: 0.3966 (ttm) REVERT: I 34 MET cc_start: 0.2958 (tmm) cc_final: 0.2670 (ppp) REVERT: I 98 ARG cc_start: 0.7922 (tpt170) cc_final: 0.7362 (tpp80) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1904 time to fit residues: 34.4543 Evaluate side-chains 86 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 417 ASN C 804 GLN C 935 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN H 37 GLN H 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.086500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.054677 restraints weight = 140515.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055621 restraints weight = 71751.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.055497 restraints weight = 47001.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055633 restraints weight = 41331.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055749 restraints weight = 38063.324| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30935 Z= 0.128 Angle : 0.547 8.804 42200 Z= 0.286 Chirality : 0.044 0.266 4878 Planarity : 0.004 0.046 5347 Dihedral : 6.208 56.115 4990 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 0.27 % Allowed : 3.75 % Favored : 95.97 % 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: 0.04 (0.14), residues: 3737 helix: 2.13 (0.21), residues: 673 sheet: 0.42 (0.17), residues: 889 loop : -0.85 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.019 0.001 TYR B1067 PHE 0.030 0.001 PHE A 338 TRP 0.009 0.001 TRP E 112 HIS 0.003 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00279 (30840) covalent geometry : angle 0.53186 (41966) SS BOND : bond 0.00274 ( 51) SS BOND : angle 0.86253 ( 102) hydrogen bonds : bond 0.04929 ( 1120) hydrogen bonds : angle 6.13043 ( 3240) link_BETA1-4 : bond 0.00377 ( 15) link_BETA1-4 : angle 1.07297 ( 45) link_NAG-ASN : bond 0.00410 ( 29) link_NAG-ASN : angle 2.67648 ( 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 111 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.8700 (p90) cc_final: 0.8435 (p90) REVERT: A 456 PHE cc_start: 0.8752 (m-80) cc_final: 0.8313 (m-80) REVERT: B 582 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8622 (tp) REVERT: B 1005 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8258 (tm-30) REVERT: D 4 MET cc_start: 0.7328 (mpp) cc_final: 0.6821 (ptp) REVERT: H 4 MET cc_start: 0.4218 (ttm) cc_final: 0.4005 (ttm) REVERT: I 98 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7829 (tpp80) outliers start: 9 outliers final: 7 residues processed: 107 average time/residue: 0.1966 time to fit residues: 34.0628 Evaluate side-chains 93 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain G residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 133 optimal weight: 30.0000 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 188 ASN B 417 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.084649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051815 restraints weight = 140928.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053681 restraints weight = 70510.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053085 restraints weight = 41265.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053421 restraints weight = 43078.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053444 restraints weight = 36909.220| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30935 Z= 0.285 Angle : 0.632 10.000 42200 Z= 0.324 Chirality : 0.045 0.288 4878 Planarity : 0.004 0.045 5347 Dihedral : 6.185 56.628 4990 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 0.58 % Allowed : 7.14 % Favored : 92.28 % 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: -0.29 (0.13), residues: 3737 helix: 1.71 (0.20), residues: 678 sheet: 0.16 (0.17), residues: 925 loop : -1.01 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 95 TYR 0.020 0.002 TYR B1067 PHE 0.023 0.002 PHE A 906 TRP 0.008 0.001 TRP I 47 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00654 (30840) covalent geometry : angle 0.61686 (41966) SS BOND : bond 0.00358 ( 51) SS BOND : angle 1.17307 ( 102) hydrogen bonds : bond 0.05309 ( 1120) hydrogen bonds : angle 5.84638 ( 3240) link_BETA1-4 : bond 0.00448 ( 15) link_BETA1-4 : angle 1.45044 ( 45) link_NAG-ASN : bond 0.00684 ( 29) link_NAG-ASN : angle 2.75651 ( 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 110 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.216 Fit side-chains REVERT: A 377 PHE cc_start: 0.8757 (p90) cc_final: 0.8545 (p90) REVERT: A 456 PHE cc_start: 0.8820 (m-80) cc_final: 0.8408 (m-80) REVERT: B 198 ASP cc_start: 0.8834 (t0) cc_final: 0.8629 (t0) REVERT: B 582 LEU cc_start: 0.8937 (mm) cc_final: 0.8604 (tp) REVERT: B 1005 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8465 (tm-30) REVERT: C 115 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: C 740 MET cc_start: 0.9136 (tpp) cc_final: 0.8888 (tpt) REVERT: D 4 MET cc_start: 0.7184 (mpp) cc_final: 0.6871 (ptp) REVERT: F 61 ARG cc_start: 0.7680 (ttp-110) cc_final: 0.7269 (ttp80) REVERT: F 76 ASN cc_start: 0.6442 (m-40) cc_final: 0.5496 (t0) REVERT: H 4 MET cc_start: 0.4133 (ttm) cc_final: 0.3880 (ttm) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.2054 time to fit residues: 35.7001 Evaluate side-chains 97 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN C1083 HIS D 38 GLN F 76 ASN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.084082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051240 restraints weight = 139873.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052889 restraints weight = 70281.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052539 restraints weight = 42893.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052834 restraints weight = 45113.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.052825 restraints weight = 37998.773| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 30935 Z= 0.310 Angle : 0.651 9.556 42200 Z= 0.332 Chirality : 0.046 0.309 4878 Planarity : 0.004 0.042 5347 Dihedral : 6.186 56.333 4990 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 0.95 % Allowed : 9.82 % Favored : 89.23 % 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: -0.50 (0.13), residues: 3737 helix: 1.52 (0.20), residues: 679 sheet: -0.02 (0.17), residues: 915 loop : -1.11 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 95 TYR 0.021 0.002 TYR B1067 PHE 0.021 0.002 PHE A 906 TRP 0.009 0.001 TRP B 258 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00708 (30840) covalent geometry : angle 0.63543 (41966) SS BOND : bond 0.00434 ( 51) SS BOND : angle 1.40988 ( 102) hydrogen bonds : bond 0.05229 ( 1120) hydrogen bonds : angle 5.71470 ( 3240) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 1.35097 ( 45) link_NAG-ASN : bond 0.00724 ( 29) link_NAG-ASN : angle 2.74542 ( 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 124 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.235 Fit side-chains REVERT: A 456 PHE cc_start: 0.8867 (m-80) cc_final: 0.8452 (m-80) REVERT: B 198 ASP cc_start: 0.8869 (t0) cc_final: 0.8605 (t0) REVERT: B 582 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8629 (tp) REVERT: B 1005 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8498 (tm-30) REVERT: C 115 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7640 (tp40) REVERT: C 740 MET cc_start: 0.9148 (tpp) cc_final: 0.8947 (tpt) REVERT: C 985 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: G 79 VAL cc_start: 0.2197 (OUTLIER) cc_final: 0.1720 (m) REVERT: H 4 MET cc_start: 0.4283 (ttm) cc_final: 0.3957 (ttm) REVERT: H 24 GLN cc_start: 0.8737 (tt0) cc_final: 0.8485 (tm-30) outliers start: 31 outliers final: 18 residues processed: 117 average time/residue: 0.1865 time to fit residues: 36.8669 Evaluate side-chains 102 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 96 ASP 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: 50.0000 chunk 332 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 349 optimal weight: 30.0000 chunk 237 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN C1083 HIS ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.084897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052312 restraints weight = 139467.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053793 restraints weight = 74931.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053983 restraints weight = 40153.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054131 restraints weight = 35865.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054354 restraints weight = 33513.410| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30935 Z= 0.172 Angle : 0.556 9.847 42200 Z= 0.284 Chirality : 0.044 0.288 4878 Planarity : 0.004 0.041 5347 Dihedral : 5.795 55.529 4990 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 0.95 % Allowed : 11.07 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.13), residues: 3737 helix: 1.85 (0.21), residues: 679 sheet: 0.08 (0.17), residues: 901 loop : -1.04 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 78 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE C 559 TRP 0.008 0.001 TRP B 104 HIS 0.006 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00389 (30840) covalent geometry : angle 0.54224 (41966) SS BOND : bond 0.00293 ( 51) SS BOND : angle 1.17168 ( 102) hydrogen bonds : bond 0.04625 ( 1120) hydrogen bonds : angle 5.42016 ( 3240) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 1.19114 ( 45) link_NAG-ASN : bond 0.00453 ( 29) link_NAG-ASN : angle 2.45638 ( 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 123 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8847 (m-80) cc_final: 0.8436 (m-80) REVERT: B 198 ASP cc_start: 0.8868 (t0) cc_final: 0.8607 (t0) REVERT: B 582 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 1005 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 115 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7430 (tp40) REVERT: C 740 MET cc_start: 0.9129 (tpp) cc_final: 0.8911 (tpt) REVERT: C 985 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8616 (m-30) REVERT: D 4 MET cc_start: 0.6423 (ptp) cc_final: 0.6086 (ptp) REVERT: G 79 VAL cc_start: 0.2199 (OUTLIER) cc_final: 0.1744 (m) REVERT: H 4 MET cc_start: 0.4244 (ttm) cc_final: 0.3912 (ttm) REVERT: H 24 GLN cc_start: 0.8703 (tt0) cc_final: 0.8479 (tm-30) outliers start: 31 outliers final: 18 residues processed: 117 average time/residue: 0.1899 time to fit residues: 37.0132 Evaluate side-chains 103 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 104 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 372 optimal weight: 30.0000 chunk 235 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 244 optimal weight: 40.0000 chunk 240 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN C1083 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.084871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052615 restraints weight = 139285.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054025 restraints weight = 70784.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053937 restraints weight = 42933.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054064 restraints weight = 42831.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054149 restraints weight = 37619.971| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30935 Z= 0.174 Angle : 0.550 9.314 42200 Z= 0.280 Chirality : 0.043 0.286 4878 Planarity : 0.004 0.041 5347 Dihedral : 5.544 55.345 4990 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.09 % Favored : 95.88 % Rotamer: Outliers : 1.13 % Allowed : 11.77 % Favored : 87.10 % 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: -0.26 (0.14), residues: 3737 helix: 1.97 (0.21), residues: 679 sheet: 0.13 (0.17), residues: 895 loop : -1.04 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.020 0.001 TYR B1067 PHE 0.021 0.001 PHE A 374 TRP 0.006 0.001 TRP B 104 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00396 (30840) covalent geometry : angle 0.53585 (41966) SS BOND : bond 0.00305 ( 51) SS BOND : angle 1.14210 ( 102) hydrogen bonds : bond 0.04454 ( 1120) hydrogen bonds : angle 5.28428 ( 3240) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.14521 ( 45) link_NAG-ASN : bond 0.00451 ( 29) link_NAG-ASN : angle 2.40540 ( 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 121 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8297 (mmm160) REVERT: A 456 PHE cc_start: 0.8846 (m-80) cc_final: 0.8440 (m-80) REVERT: B 198 ASP cc_start: 0.8902 (t0) cc_final: 0.8629 (t0) REVERT: B 582 LEU cc_start: 0.8938 (mm) cc_final: 0.8672 (tp) REVERT: B 1005 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 115 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7435 (tp40) REVERT: C 740 MET cc_start: 0.9145 (tpp) cc_final: 0.8920 (tpt) REVERT: C 959 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9219 (mp) REVERT: C 985 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8621 (m-30) REVERT: D 4 MET cc_start: 0.6490 (ptp) cc_final: 0.6125 (ptp) REVERT: G 79 VAL cc_start: 0.2093 (OUTLIER) cc_final: 0.1647 (m) REVERT: H 4 MET cc_start: 0.4250 (ttm) cc_final: 0.3919 (ttm) REVERT: H 24 GLN cc_start: 0.8680 (tt0) cc_final: 0.8464 (tm-30) outliers start: 37 outliers final: 25 residues processed: 116 average time/residue: 0.1697 time to fit residues: 33.2522 Evaluate side-chains 110 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 50 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 262 optimal weight: 0.0170 chunk 126 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN C1083 HIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.085455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053239 restraints weight = 139031.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.055016 restraints weight = 68610.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054801 restraints weight = 39305.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054996 restraints weight = 39457.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055019 restraints weight = 35782.879| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30935 Z= 0.119 Angle : 0.520 12.888 42200 Z= 0.264 Chirality : 0.043 0.268 4878 Planarity : 0.004 0.042 5347 Dihedral : 5.230 55.123 4990 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 1.10 % Allowed : 12.26 % Favored : 86.64 % 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: -0.16 (0.14), residues: 3737 helix: 2.14 (0.21), residues: 674 sheet: 0.17 (0.17), residues: 930 loop : -1.00 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.020 0.001 TYR B1067 PHE 0.021 0.001 PHE A 374 TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00265 (30840) covalent geometry : angle 0.50788 (41966) SS BOND : bond 0.00259 ( 51) SS BOND : angle 1.01969 ( 102) hydrogen bonds : bond 0.04084 ( 1120) hydrogen bonds : angle 5.10029 ( 3240) link_BETA1-4 : bond 0.00335 ( 15) link_BETA1-4 : angle 1.04923 ( 45) link_NAG-ASN : bond 0.00352 ( 29) link_NAG-ASN : angle 2.26030 ( 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 126 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8353 (mmm160) REVERT: A 456 PHE cc_start: 0.8831 (m-80) cc_final: 0.8430 (m-80) REVERT: B 198 ASP cc_start: 0.8822 (t0) cc_final: 0.8570 (t0) REVERT: B 582 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8647 (tp) REVERT: B 1005 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 115 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: C 740 MET cc_start: 0.9158 (tpp) cc_final: 0.8934 (tpt) REVERT: C 985 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8609 (m-30) REVERT: D 4 MET cc_start: 0.6471 (ptp) cc_final: 0.6172 (ptp) REVERT: G 79 VAL cc_start: 0.2081 (OUTLIER) cc_final: 0.1647 (m) REVERT: H 4 MET cc_start: 0.4202 (ttm) cc_final: 0.3867 (ttm) REVERT: H 24 GLN cc_start: 0.8637 (tt0) cc_final: 0.8434 (tm-30) outliers start: 36 outliers final: 26 residues processed: 121 average time/residue: 0.1788 time to fit residues: 36.5568 Evaluate side-chains 113 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 262 optimal weight: 0.0470 chunk 62 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 156 optimal weight: 3.9990 chunk 350 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.085075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052839 restraints weight = 139914.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054279 restraints weight = 74731.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054195 restraints weight = 44395.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054196 restraints weight = 41538.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054340 restraints weight = 38476.117| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2021 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= 0.158 Angle : 0.534 12.215 42200 Z= 0.271 Chirality : 0.043 0.274 4878 Planarity : 0.004 0.043 5347 Dihedral : 5.153 55.264 4990 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 1.37 % Allowed : 12.56 % Favored : 86.06 % 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: -0.17 (0.14), residues: 3737 helix: 2.12 (0.21), residues: 674 sheet: 0.16 (0.17), residues: 897 loop : -1.00 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.020 0.001 TYR B1067 PHE 0.026 0.001 PHE A 374 TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00361 (30840) covalent geometry : angle 0.52195 (41966) SS BOND : bond 0.00284 ( 51) SS BOND : angle 1.03392 ( 102) hydrogen bonds : bond 0.04174 ( 1120) hydrogen bonds : angle 5.07433 ( 3240) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.08137 ( 45) link_NAG-ASN : bond 0.00413 ( 29) link_NAG-ASN : angle 2.29796 ( 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 129 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8352 (mmm160) REVERT: A 456 PHE cc_start: 0.8839 (m-80) cc_final: 0.8442 (m-80) REVERT: B 198 ASP cc_start: 0.8882 (t0) cc_final: 0.8657 (t0) REVERT: B 582 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 1005 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 115 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7180 (tp40) REVERT: C 740 MET cc_start: 0.9170 (tpp) cc_final: 0.8950 (tpt) REVERT: C 959 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9202 (mp) REVERT: C 985 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8602 (m-30) REVERT: D 4 MET cc_start: 0.6513 (ptp) cc_final: 0.6204 (ptp) REVERT: E 61 TYR cc_start: 0.9301 (m-10) cc_final: 0.9052 (m-10) REVERT: G 79 VAL cc_start: 0.2066 (OUTLIER) cc_final: 0.1620 (m) REVERT: H 1 ASP cc_start: 0.8244 (m-30) cc_final: 0.7894 (p0) REVERT: H 4 MET cc_start: 0.4127 (ttm) cc_final: 0.3784 (ttm) REVERT: H 24 GLN cc_start: 0.8634 (tt0) cc_final: 0.8429 (tm-30) outliers start: 45 outliers final: 30 residues processed: 123 average time/residue: 0.1823 time to fit residues: 37.8806 Evaluate side-chains 116 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 82 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 173 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 293 optimal weight: 0.0050 chunk 197 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN C 354 ASN C1054 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.085891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053906 restraints weight = 139385.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055462 restraints weight = 72901.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055370 restraints weight = 43349.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055487 restraints weight = 42201.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055593 restraints weight = 36655.137| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 30935 Z= 0.102 Angle : 0.516 11.577 42200 Z= 0.261 Chirality : 0.043 0.354 4878 Planarity : 0.004 0.044 5347 Dihedral : 4.864 54.858 4990 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 0.95 % Allowed : 13.21 % Favored : 85.85 % 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: -0.06 (0.14), residues: 3737 helix: 2.23 (0.21), residues: 673 sheet: 0.26 (0.17), residues: 911 loop : -0.95 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.020 0.001 TYR B1067 PHE 0.028 0.001 PHE A 374 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00228 (30840) covalent geometry : angle 0.50261 (41966) SS BOND : bond 0.00273 ( 51) SS BOND : angle 1.09112 ( 102) hydrogen bonds : bond 0.03800 ( 1120) hydrogen bonds : angle 4.89840 ( 3240) link_BETA1-4 : bond 0.00372 ( 15) link_BETA1-4 : angle 0.97594 ( 45) link_NAG-ASN : bond 0.00356 ( 29) link_NAG-ASN : angle 2.36016 ( 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 122 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (mmm160) REVERT: A 456 PHE cc_start: 0.8816 (m-80) cc_final: 0.8424 (m-80) REVERT: B 582 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8585 (tp) REVERT: B 1005 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8213 (tm-30) REVERT: C 115 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: C 740 MET cc_start: 0.9068 (tpp) cc_final: 0.8803 (tpt) REVERT: C 985 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8583 (m-30) REVERT: D 4 MET cc_start: 0.6465 (ptp) cc_final: 0.6170 (ptp) REVERT: E 61 TYR cc_start: 0.9296 (m-10) cc_final: 0.9055 (m-10) REVERT: G 79 VAL cc_start: 0.2028 (OUTLIER) cc_final: 0.1596 (m) REVERT: H 1 ASP cc_start: 0.8307 (m-30) cc_final: 0.7939 (p0) REVERT: H 4 MET cc_start: 0.4030 (ttm) cc_final: 0.3702 (ttm) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.1964 time to fit residues: 38.0724 Evaluate side-chains 108 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 34 optimal weight: 5.9990 chunk 358 optimal weight: 50.0000 chunk 364 optimal weight: 6.9990 chunk 176 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 305 optimal weight: 0.5980 chunk 271 optimal weight: 2.9990 chunk 321 optimal weight: 0.9990 chunk 255 optimal weight: 0.5980 chunk 289 optimal weight: 0.0370 chunk 307 optimal weight: 7.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 125 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.086048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054071 restraints weight = 139049.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.056110 restraints weight = 68241.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055506 restraints weight = 37580.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.055649 restraints weight = 40217.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.055792 restraints weight = 35740.872| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 30935 Z= 0.100 Angle : 0.512 11.505 42200 Z= 0.260 Chirality : 0.043 0.437 4878 Planarity : 0.004 0.044 5347 Dihedral : 4.713 54.869 4990 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 0.73 % Allowed : 13.48 % Favored : 85.79 % 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: -0.02 (0.14), residues: 3737 helix: 2.22 (0.21), residues: 680 sheet: 0.26 (0.17), residues: 894 loop : -0.89 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 355 TYR 0.019 0.001 TYR B1067 PHE 0.032 0.001 PHE A 374 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00223 (30840) covalent geometry : angle 0.49984 (41966) SS BOND : bond 0.00253 ( 51) SS BOND : angle 1.10413 ( 102) hydrogen bonds : bond 0.03644 ( 1120) hydrogen bonds : angle 4.82220 ( 3240) link_BETA1-4 : bond 0.00380 ( 15) link_BETA1-4 : angle 0.97533 ( 45) link_NAG-ASN : bond 0.00335 ( 29) link_NAG-ASN : angle 2.18025 ( 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 115 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8809 (m-80) cc_final: 0.8421 (m-80) REVERT: B 238 PHE cc_start: 0.8383 (p90) cc_final: 0.8096 (p90) REVERT: B 582 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 1005 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 115 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7328 (tp40) REVERT: C 985 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: E 61 TYR cc_start: 0.9292 (m-10) cc_final: 0.9049 (m-10) REVERT: G 79 VAL cc_start: 0.2040 (OUTLIER) cc_final: 0.1606 (m) REVERT: H 1 ASP cc_start: 0.8333 (m-30) cc_final: 0.7930 (p0) REVERT: H 4 MET cc_start: 0.3995 (ttm) cc_final: 0.3764 (ttm) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.1866 time to fit residues: 34.8577 Evaluate side-chains 105 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 121 optimal weight: 4.9990 chunk 364 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 201 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 337 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C1054 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.084050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051419 restraints weight = 140993.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053029 restraints weight = 71636.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052440 restraints weight = 44152.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.052789 restraints weight = 48787.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052806 restraints weight = 40849.833| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30935 Z= 0.303 Angle : 0.658 12.206 42200 Z= 0.333 Chirality : 0.046 0.298 4878 Planarity : 0.004 0.043 5347 Dihedral : 5.317 56.270 4990 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 0.98 % Allowed : 13.54 % Favored : 85.48 % 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: -0.33 (0.14), residues: 3737 helix: 1.75 (0.21), residues: 685 sheet: 0.07 (0.17), residues: 907 loop : -1.03 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 995 TYR 0.023 0.002 TYR B1067 PHE 0.033 0.002 PHE A 374 TRP 0.012 0.001 TRP B 258 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00697 (30840) covalent geometry : angle 0.64438 (41966) SS BOND : bond 0.00345 ( 51) SS BOND : angle 1.43744 ( 102) hydrogen bonds : bond 0.04892 ( 1120) hydrogen bonds : angle 5.23779 ( 3240) link_BETA1-4 : bond 0.00321 ( 15) link_BETA1-4 : angle 1.28153 ( 45) link_NAG-ASN : bond 0.00724 ( 29) link_NAG-ASN : angle 2.56505 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5057.55 seconds wall clock time: 88 minutes 27.33 seconds (5307.33 seconds total)