Starting phenix.real_space_refine on Thu Feb 5 03:33:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejj_28184/02_2026/8ejj_28184.cif" } resolution = 3.22 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= 0.029 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 114 5.16 5 C 9276 2.51 5 N 2367 2.21 5 O 3105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14862 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "I" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "a" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "b" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "c" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "h" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "l" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Y" 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.08, per 1000 atoms: 0.27 Number of scatterers: 14862 At special positions: 0 Unit cell: (131.1, 129.95, 102.35, 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 114 16.00 O 3105 8.00 N 2367 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.15 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.15 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.15 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.15 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.02 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 111D" distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.02 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 111D" distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.01 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.01 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.01 Simple disulfide: pdb=" SG CYS h 23 " - pdb=" SG CYS h 104 " distance=2.02 Simple disulfide: pdb=" SG CYS h 110 " - pdb=" SG CYS h 111D" distance=2.02 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Z 4 " - " MAN Z 5 " " MAN f 4 " - " MAN f 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA D 3 " - " MAN l 201 " " BMA N 3 " - " MAN N 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " BMA N 3 " - " MAN N 5 " " BMA T 3 " - " MAN T 5 " " BMA Z 3 " - " MAN Z 6 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 T 2 " - " BMA T 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG m 1 " - " NAG m 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG B 301 " - " ASN B 99 " " NAG C 301 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG K 1 " - " ASN A 167 " " NAG M 1 " - " ASN A 224 " " NAG N 1 " - " ASN B 79 " " NAG O 1 " - " ASN B 89 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 167 " " NAG S 1 " - " ASN B 224 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN a 365 " " NAG a 501 " - " ASN a 395 " " NAG b 501 " - " ASN b 395 " " NAG c 501 " - " ASN c 395 " " NAG d 1 " - " ASN a 373 " " NAG e 1 " - " ASN a 390 " " NAG f 1 " - " ASN b 365 " " NAG g 1 " - " ASN b 373 " " NAG i 1 " - " ASN b 390 " " NAG j 1 " - " ASN c 365 " " NAG k 1 " - " ASN c 373 " " NAG m 1 " - " ASN c 390 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 532.3 milliseconds 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 27 sheets defined 27.9% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 removed outlier: 4.005A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 removed outlier: 4.004A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 183 through 195 removed outlier: 4.214A pdb=" N GLN B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.006A pdb=" N ILE C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 183 through 195 removed outlier: 4.215A pdb=" N GLN C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 111A through 112 removed outlier: 3.640A pdb=" N CYS H 111D" --> pdb=" O SER H 111A" (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 74 No H-bonds generated for 'chain 'I' and resid 71 through 74' Processing helix chain 'I' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS I 111D" --> pdb=" O SER I 111A" (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 398 Processing helix chain 'a' and resid 399 through 423 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU b 344 " --> pdb=" O ALA b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.930A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 423 Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.681A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.929A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 423 Processing helix chain 'h' and resid 71 through 74 No H-bonds generated for 'chain 'h' and resid 71 through 74' Processing helix chain 'h' and resid 111A through 112 removed outlier: 3.641A pdb=" N CYS h 111D" --> pdb=" O SER h 111A" (cutoff:3.500A) Processing helix chain 'l' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR A 87 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 235 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 87 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG B 235 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.507A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR C 87 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 235 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP H 52 " --> pdb=" O ARG H 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 19 through 22 Processing sheet with id=AA9, first strand: chain 'I' and resid 12 through 13 removed outlier: 6.105A pdb=" N ARG I 43 " --> pdb=" O TRP I 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP I 52 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 22 Processing sheet with id=AB2, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.546A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AB4, first strand: chain 'J' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP L 41 " --> pdb=" O VAL L 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB8, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB9, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AC1, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AC2, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AC3, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AC4, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AC5, first strand: chain 'h' and resid 12 through 13 removed outlier: 6.106A pdb=" N ARG h 43 " --> pdb=" O TRP h 52 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP h 52 " --> pdb=" O ARG h 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 19 through 22 Processing sheet with id=AC7, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.548A pdb=" N TRP l 41 " --> pdb=" O VAL l 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AC9, first strand: chain 'l' and resid 19 through 24 579 hydrogen bonds defined for protein. 1449 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: 2.72 Time building geometry restraints manager: 2.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3699 1.33 - 1.47: 5128 1.47 - 1.61: 6185 1.61 - 1.75: 37 1.75 - 1.90: 134 Bond restraints: 15183 Sorted by residual: bond pdb=" CB HIS b 354 " pdb=" CG HIS b 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" CB LEU l 127 " pdb=" CG LEU l 127 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS A 141 " pdb=" CG HIS A 141 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.66e+01 bond pdb=" CB LEU L 127 " pdb=" CG LEU L 127 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 15178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17471 2.38 - 4.76: 2637 4.76 - 7.14: 422 7.14 - 9.51: 65 9.51 - 11.89: 12 Bond angle restraints: 20607 Sorted by residual: angle pdb=" N PRO H 45 " pdb=" CA PRO H 45 " pdb=" C PRO H 45 " ideal model delta sigma weight residual 110.47 102.96 7.51 9.60e-01 1.09e+00 6.12e+01 angle pdb=" N VAL H 76 " pdb=" CA VAL H 76 " pdb=" C VAL H 76 " ideal model delta sigma weight residual 108.11 118.92 -10.81 1.40e+00 5.10e-01 5.96e+01 angle pdb=" N PRO I 45 " pdb=" CA PRO I 45 " pdb=" C PRO I 45 " ideal model delta sigma weight residual 110.47 103.07 7.40 9.60e-01 1.09e+00 5.93e+01 angle pdb=" N PRO h 45 " pdb=" CA PRO h 45 " pdb=" C PRO h 45 " ideal model delta sigma weight residual 110.47 103.09 7.38 9.60e-01 1.09e+00 5.92e+01 angle pdb=" N VAL I 76 " pdb=" CA VAL I 76 " pdb=" C VAL I 76 " ideal model delta sigma weight residual 108.11 118.85 -10.74 1.40e+00 5.10e-01 5.88e+01 ... (remaining 20602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 9774 21.35 - 42.71: 225 42.71 - 64.06: 75 64.06 - 85.41: 54 85.41 - 106.77: 45 Dihedral angle restraints: 10173 sinusoidal: 5103 harmonic: 5070 Sorted by residual: dihedral pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.46 -59.54 1 1.00e+01 1.00e-02 4.73e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.61 -59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS C 180 " pdb=" SG CYS C 180 " pdb=" SG CYS C 212 " pdb=" CB CYS C 212 " ideal model delta sinusoidal sigma weight residual -86.00 -26.67 -59.33 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 10170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1552 0.103 - 0.206: 591 0.206 - 0.309: 225 0.309 - 0.412: 114 0.412 - 0.516: 38 Chirality restraints: 2520 Sorted by residual: chirality pdb=" C1 NAG i 2 " pdb=" O4 NAG i 1 " pdb=" C2 NAG i 2 " pdb=" O5 NAG i 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 BMA g 3 " pdb=" O4 NAG g 2 " pdb=" C2 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 BMA d 3 " pdb=" O4 NAG d 2 " pdb=" C2 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 2517 not shown) Planarity restraints: 2523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 89 " -0.056 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" CG ASN C 89 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 89 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 89 " 0.088 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 89 " 0.056 2.00e-02 2.50e+03 5.74e-02 4.12e+01 pdb=" CG ASN B 89 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 89 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 89 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 89 " -0.056 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN A 89 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 89 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 89 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.069 2.00e-02 2.50e+03 ... (remaining 2520 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 5960 2.90 - 3.40: 13477 3.40 - 3.90: 25244 3.90 - 4.40: 29786 4.40 - 4.90: 47733 Nonbonded interactions: 122200 Sorted by model distance: nonbonded pdb=" OH TYR h 38 " pdb=" O CYS h 111D" model vdw 2.394 3.040 nonbonded pdb=" OH TYR H 38 " pdb=" O CYS H 111D" model vdw 2.394 3.040 nonbonded pdb=" OH TYR I 38 " pdb=" O CYS I 111D" model vdw 2.394 3.040 nonbonded pdb=" O4 MAN j 4 " pdb=" O6 MAN j 4 " model vdw 2.395 3.040 nonbonded pdb=" O4 MAN Z 4 " pdb=" O6 MAN Z 4 " model vdw 2.396 3.040 ... (remaining 122195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'e' selection = chain 'i' selection = chain 'm' } ncs_group { reference = (chain 'G' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'h' } ncs_group { reference = chain 'J' selection = chain 'L' selection = (chain 'l' and resid 2 through 127) } ncs_group { reference = chain 'N' selection = chain 'T' } ncs_group { reference = chain 'Z' selection = chain 'f' selection = chain 'j' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 : 0.025 0.138 15300 Z= 1.286 Angle : 2.018 53.110 20928 Z= 1.213 Chirality : 0.146 0.516 2520 Planarity : 0.009 0.079 2490 Dihedral : 13.946 106.765 6843 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.28 (0.20), residues: 1713 helix: -1.15 (0.23), residues: 369 sheet: 0.95 (0.26), residues: 450 loop : 0.56 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 75 TYR 0.063 0.008 TYR H 26 PHE 0.030 0.007 PHE h 115 TRP 0.039 0.010 TRP H 52 HIS 0.010 0.002 HIS c 354 Details of bonding type rmsd covalent geometry : bond 0.02410 (15183) covalent geometry : angle 1.79681 (20607) SS BOND : bond 0.04519 ( 30) SS BOND : angle 14.77117 ( 60) hydrogen bonds : bond 0.16883 ( 561) hydrogen bonds : angle 7.46701 ( 1449) link_ALPHA1-2 : bond 0.07680 ( 3) link_ALPHA1-2 : angle 4.68004 ( 9) link_ALPHA1-3 : bond 0.09704 ( 6) link_ALPHA1-3 : angle 7.27547 ( 18) link_ALPHA1-6 : bond 0.05442 ( 6) link_ALPHA1-6 : angle 3.58101 ( 18) link_BETA1-4 : bond 0.06988 ( 36) link_BETA1-4 : angle 5.72432 ( 108) link_BETA1-6 : bond 0.05237 ( 3) link_BETA1-6 : angle 2.32469 ( 9) link_NAG-ASN : bond 0.07143 ( 33) link_NAG-ASN : angle 2.58794 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8969 (mmp) cc_final: 0.8744 (mmt) REVERT: A 115 HIS cc_start: 0.7304 (m170) cc_final: 0.7102 (m90) REVERT: B 115 HIS cc_start: 0.7382 (m170) cc_final: 0.7135 (m-70) REVERT: J 67 ARG cc_start: 0.8902 (ttp-110) cc_final: 0.8507 (ttm110) REVERT: L 67 ARG cc_start: 0.8766 (ttp-110) cc_final: 0.8438 (ttm110) REVERT: c 332 MET cc_start: 0.8178 (tmt) cc_final: 0.7120 (tmt) REVERT: c 401 ASP cc_start: 0.7665 (m-30) cc_final: 0.7438 (m-30) REVERT: c 410 MET cc_start: 0.8516 (mtp) cc_final: 0.8222 (mtp) REVERT: c 419 TYR cc_start: 0.8216 (t80) cc_final: 0.7967 (t80) REVERT: l 18 THR cc_start: 0.8356 (m) cc_final: 0.8040 (p) REVERT: l 67 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8213 (ttm110) REVERT: l 123 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8031 (ttmm) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1669 time to fit residues: 84.0584 Evaluate side-chains 197 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 58 HIS ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 354 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 324 GLN ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 324 GLN h 58 HIS ** l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086363 restraints weight = 27740.053| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.41 r_work: 0.3275 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15300 Z= 0.187 Angle : 0.821 10.259 20928 Z= 0.397 Chirality : 0.050 0.245 2520 Planarity : 0.005 0.044 2490 Dihedral : 11.094 78.285 3657 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.49 % Allowed : 6.56 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.63 (0.21), residues: 1713 helix: 0.37 (0.26), residues: 366 sheet: 0.99 (0.26), residues: 432 loop : 0.28 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 193 TYR 0.019 0.002 TYR L 115 PHE 0.018 0.002 PHE A 117 TRP 0.029 0.002 TRP C 210 HIS 0.004 0.001 HIS c 305 Details of bonding type rmsd covalent geometry : bond 0.00426 (15183) covalent geometry : angle 0.75069 (20607) SS BOND : bond 0.00400 ( 30) SS BOND : angle 1.33197 ( 60) hydrogen bonds : bond 0.05148 ( 561) hydrogen bonds : angle 5.50898 ( 1449) link_ALPHA1-2 : bond 0.00027 ( 3) link_ALPHA1-2 : angle 2.38155 ( 9) link_ALPHA1-3 : bond 0.02758 ( 6) link_ALPHA1-3 : angle 3.12342 ( 18) link_ALPHA1-6 : bond 0.00908 ( 6) link_ALPHA1-6 : angle 1.51772 ( 18) link_BETA1-4 : bond 0.00880 ( 36) link_BETA1-4 : angle 3.65719 ( 108) link_BETA1-6 : bond 0.00299 ( 3) link_BETA1-6 : angle 1.68214 ( 9) link_NAG-ASN : bond 0.00569 ( 33) link_NAG-ASN : angle 2.53039 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7351 (m170) cc_final: 0.7142 (m90) REVERT: A 122 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: A 151 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: A 204 ASP cc_start: 0.8519 (t0) cc_final: 0.8263 (t0) REVERT: B 75 MET cc_start: 0.8841 (mtm) cc_final: 0.8592 (mtp) REVERT: B 115 HIS cc_start: 0.7369 (m170) cc_final: 0.6998 (m90) REVERT: B 151 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: C 180 CYS cc_start: 0.5545 (OUTLIER) cc_final: 0.5252 (t) REVERT: C 204 ASP cc_start: 0.8702 (t0) cc_final: 0.8302 (t0) REVERT: C 211 ASP cc_start: 0.7019 (p0) cc_final: 0.6717 (t0) REVERT: J 123 LYS cc_start: 0.8357 (tttt) cc_final: 0.8061 (mttp) REVERT: L 67 ARG cc_start: 0.8914 (ttp-110) cc_final: 0.8626 (ttm110) REVERT: L 123 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8282 (ttmm) REVERT: b 306 ASP cc_start: 0.8569 (p0) cc_final: 0.8343 (p0) REVERT: b 321 GLN cc_start: 0.8388 (mt0) cc_final: 0.8183 (mt0) REVERT: b 332 MET cc_start: 0.8199 (tmt) cc_final: 0.7932 (tmm) REVERT: b 333 SER cc_start: 0.7909 (t) cc_final: 0.7448 (p) REVERT: l 123 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8212 (mmtm) outliers start: 23 outliers final: 12 residues processed: 255 average time/residue: 0.1503 time to fit residues: 54.3191 Evaluate side-chains 218 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS B 93 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 GLN l 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073589 restraints weight = 28100.473| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.65 r_work: 0.2964 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15300 Z= 0.163 Angle : 0.741 9.048 20928 Z= 0.355 Chirality : 0.046 0.247 2520 Planarity : 0.005 0.041 2490 Dihedral : 9.401 71.873 3657 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.30 % Allowed : 8.32 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.55 (0.20), residues: 1713 helix: 0.99 (0.27), residues: 372 sheet: 0.93 (0.25), residues: 441 loop : -0.11 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.016 0.001 TYR h 26 PHE 0.013 0.001 PHE A 117 TRP 0.046 0.002 TRP C 210 HIS 0.008 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00373 (15183) covalent geometry : angle 0.67294 (20607) SS BOND : bond 0.00396 ( 30) SS BOND : angle 2.17694 ( 60) hydrogen bonds : bond 0.04354 ( 561) hydrogen bonds : angle 5.06554 ( 1449) link_ALPHA1-2 : bond 0.00052 ( 3) link_ALPHA1-2 : angle 2.25882 ( 9) link_ALPHA1-3 : bond 0.02592 ( 6) link_ALPHA1-3 : angle 3.25481 ( 18) link_ALPHA1-6 : bond 0.00642 ( 6) link_ALPHA1-6 : angle 1.65058 ( 18) link_BETA1-4 : bond 0.00810 ( 36) link_BETA1-4 : angle 3.07703 ( 108) link_BETA1-6 : bond 0.00312 ( 3) link_BETA1-6 : angle 1.48736 ( 9) link_NAG-ASN : bond 0.00410 ( 33) link_NAG-ASN : angle 2.32536 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.7231 (m170) cc_final: 0.6982 (m90) REVERT: A 204 ASP cc_start: 0.8579 (t0) cc_final: 0.8278 (t0) REVERT: B 115 HIS cc_start: 0.7149 (m170) cc_final: 0.6772 (m90) REVERT: C 115 HIS cc_start: 0.7087 (m170) cc_final: 0.6858 (m90) REVERT: C 204 ASP cc_start: 0.8519 (t0) cc_final: 0.8176 (t0) REVERT: C 228 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8092 (mm-30) REVERT: I 48 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8351 (mttm) REVERT: J 123 LYS cc_start: 0.8578 (tttt) cc_final: 0.8278 (mttp) REVERT: L 123 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8248 (ttmm) REVERT: a 306 ASP cc_start: 0.8739 (p0) cc_final: 0.8451 (p0) REVERT: b 321 GLN cc_start: 0.8375 (mt0) cc_final: 0.8123 (mt0) REVERT: b 379 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8399 (mmm-85) REVERT: h 29 SER cc_start: 0.8077 (m) cc_final: 0.7826 (t) REVERT: h 94 VAL cc_start: 0.8685 (p) cc_final: 0.8481 (p) REVERT: l 123 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8172 (mmtm) outliers start: 20 outliers final: 13 residues processed: 213 average time/residue: 0.1384 time to fit residues: 42.9542 Evaluate side-chains 195 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain a residue 283 TRP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.092846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.073546 restraints weight = 27945.825| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.70 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15300 Z= 0.131 Angle : 0.688 8.690 20928 Z= 0.327 Chirality : 0.045 0.225 2520 Planarity : 0.004 0.042 2490 Dihedral : 7.969 63.115 3657 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 8.90 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.54 (0.20), residues: 1713 helix: 1.30 (0.28), residues: 369 sheet: 0.89 (0.25), residues: 432 loop : -0.25 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.016 0.001 TYR b 419 PHE 0.011 0.001 PHE A 117 TRP 0.041 0.001 TRP A 210 HIS 0.009 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00293 (15183) covalent geometry : angle 0.62454 (20607) SS BOND : bond 0.00450 ( 30) SS BOND : angle 2.33438 ( 60) hydrogen bonds : bond 0.03709 ( 561) hydrogen bonds : angle 4.89943 ( 1449) link_ALPHA1-2 : bond 0.00117 ( 3) link_ALPHA1-2 : angle 2.16431 ( 9) link_ALPHA1-3 : bond 0.02265 ( 6) link_ALPHA1-3 : angle 2.86412 ( 18) link_ALPHA1-6 : bond 0.00788 ( 6) link_ALPHA1-6 : angle 1.72015 ( 18) link_BETA1-4 : bond 0.00723 ( 36) link_BETA1-4 : angle 2.76345 ( 108) link_BETA1-6 : bond 0.00321 ( 3) link_BETA1-6 : angle 1.49162 ( 9) link_NAG-ASN : bond 0.00342 ( 33) link_NAG-ASN : angle 2.16908 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6920 (m170) cc_final: 0.6702 (m90) REVERT: A 204 ASP cc_start: 0.8446 (t0) cc_final: 0.8102 (t0) REVERT: B 115 HIS cc_start: 0.6924 (m170) cc_final: 0.6560 (m90) REVERT: C 115 HIS cc_start: 0.6832 (m170) cc_final: 0.6622 (m-70) REVERT: C 204 ASP cc_start: 0.8529 (t0) cc_final: 0.8230 (t0) REVERT: C 228 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8023 (mm-30) REVERT: I 85 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7392 (t0) REVERT: J 123 LYS cc_start: 0.8430 (tttt) cc_final: 0.8082 (mttp) REVERT: L 123 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7895 (mttm) REVERT: a 306 ASP cc_start: 0.8654 (p0) cc_final: 0.8328 (p0) REVERT: b 321 GLN cc_start: 0.8138 (mt0) cc_final: 0.7874 (mt0) REVERT: b 379 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8273 (mmm-85) REVERT: c 324 GLN cc_start: 0.8748 (mt0) cc_final: 0.8390 (mt0) REVERT: l 123 LYS cc_start: 0.8400 (ttmm) cc_final: 0.7931 (mmtm) outliers start: 32 outliers final: 23 residues processed: 217 average time/residue: 0.1391 time to fit residues: 43.9897 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 152 optimal weight: 0.0670 chunk 81 optimal weight: 0.0070 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** 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 = 0.3431 r_free = 0.3431 target = 0.092966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073639 restraints weight = 27913.886| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.72 r_work: 0.2962 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15300 Z= 0.121 Angle : 0.663 8.238 20928 Z= 0.314 Chirality : 0.044 0.226 2520 Planarity : 0.004 0.042 2490 Dihedral : 7.306 58.208 3657 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.88 % Allowed : 10.14 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.46 (0.20), residues: 1713 helix: 1.46 (0.28), residues: 369 sheet: 0.75 (0.25), residues: 441 loop : -0.37 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 379 TYR 0.015 0.001 TYR b 419 PHE 0.010 0.001 PHE A 117 TRP 0.022 0.001 TRP C 210 HIS 0.004 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00268 (15183) covalent geometry : angle 0.60599 (20607) SS BOND : bond 0.00363 ( 30) SS BOND : angle 1.97752 ( 60) hydrogen bonds : bond 0.03479 ( 561) hydrogen bonds : angle 4.80975 ( 1449) link_ALPHA1-2 : bond 0.00108 ( 3) link_ALPHA1-2 : angle 2.12761 ( 9) link_ALPHA1-3 : bond 0.02167 ( 6) link_ALPHA1-3 : angle 2.64488 ( 18) link_ALPHA1-6 : bond 0.00765 ( 6) link_ALPHA1-6 : angle 1.66257 ( 18) link_BETA1-4 : bond 0.00698 ( 36) link_BETA1-4 : angle 2.56910 ( 108) link_BETA1-6 : bond 0.00333 ( 3) link_BETA1-6 : angle 1.46281 ( 9) link_NAG-ASN : bond 0.00333 ( 33) link_NAG-ASN : angle 2.14437 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6801 (m170) cc_final: 0.6570 (m90) REVERT: A 151 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: A 204 ASP cc_start: 0.8507 (t0) cc_final: 0.8146 (t0) REVERT: B 115 HIS cc_start: 0.6912 (m170) cc_final: 0.6529 (m90) REVERT: C 115 HIS cc_start: 0.6719 (m170) cc_final: 0.6468 (m90) REVERT: C 204 ASP cc_start: 0.8535 (t0) cc_final: 0.8264 (t0) REVERT: C 228 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7935 (mm-30) REVERT: H 14 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7357 (mmtt) REVERT: I 48 LYS cc_start: 0.8662 (mttp) cc_final: 0.8411 (mttm) REVERT: J 123 LYS cc_start: 0.8415 (tttt) cc_final: 0.8060 (mttp) REVERT: L 123 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7904 (mttm) REVERT: b 321 GLN cc_start: 0.8120 (mt0) cc_final: 0.7806 (mt0) REVERT: b 379 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8388 (mmm-85) REVERT: b 420 MET cc_start: 0.8769 (mmm) cc_final: 0.8311 (tmm) outliers start: 29 outliers final: 21 residues processed: 213 average time/residue: 0.1333 time to fit residues: 41.7868 Evaluate side-chains 208 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 65 optimal weight: 0.3980 chunk 151 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 109 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 66 ASN ** 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 = 0.3411 r_free = 0.3411 target = 0.091765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.072602 restraints weight = 27854.345| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.82 r_work: 0.2918 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15300 Z= 0.139 Angle : 0.654 7.857 20928 Z= 0.309 Chirality : 0.044 0.227 2520 Planarity : 0.004 0.048 2490 Dihedral : 6.889 53.585 3657 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.27 % Allowed : 9.88 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.41 (0.20), residues: 1713 helix: 1.51 (0.28), residues: 369 sheet: 0.69 (0.25), residues: 441 loop : -0.43 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.015 0.001 TYR b 419 PHE 0.012 0.001 PHE A 117 TRP 0.033 0.001 TRP B 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00320 (15183) covalent geometry : angle 0.60231 (20607) SS BOND : bond 0.00384 ( 30) SS BOND : angle 1.57628 ( 60) hydrogen bonds : bond 0.03487 ( 561) hydrogen bonds : angle 4.75760 ( 1449) link_ALPHA1-2 : bond 0.00175 ( 3) link_ALPHA1-2 : angle 2.15970 ( 9) link_ALPHA1-3 : bond 0.02037 ( 6) link_ALPHA1-3 : angle 2.46709 ( 18) link_ALPHA1-6 : bond 0.00749 ( 6) link_ALPHA1-6 : angle 1.62033 ( 18) link_BETA1-4 : bond 0.00658 ( 36) link_BETA1-4 : angle 2.46865 ( 108) link_BETA1-6 : bond 0.00313 ( 3) link_BETA1-6 : angle 1.49451 ( 9) link_NAG-ASN : bond 0.00304 ( 33) link_NAG-ASN : angle 2.13606 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6789 (m170) cc_final: 0.6565 (m90) REVERT: A 151 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: A 204 ASP cc_start: 0.8444 (t0) cc_final: 0.8033 (t0) REVERT: B 115 HIS cc_start: 0.7065 (m170) cc_final: 0.6739 (m90) REVERT: C 125 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8812 (ttmm) REVERT: C 185 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8141 (t0) REVERT: C 204 ASP cc_start: 0.8552 (t0) cc_final: 0.8305 (t0) REVERT: C 228 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7972 (mm-30) REVERT: J 123 LYS cc_start: 0.8434 (tttt) cc_final: 0.8108 (mttp) REVERT: L 123 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7962 (mttm) REVERT: b 321 GLN cc_start: 0.8157 (mt0) cc_final: 0.7864 (mt0) REVERT: b 379 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8403 (mmm-85) REVERT: c 324 GLN cc_start: 0.8723 (mt0) cc_final: 0.8392 (mt0) REVERT: l 123 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7975 (mttm) outliers start: 35 outliers final: 25 residues processed: 208 average time/residue: 0.1321 time to fit residues: 40.4876 Evaluate side-chains 207 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 100 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077306 restraints weight = 27455.115| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.55 r_work: 0.3055 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 15300 Z= 0.150 Angle : 0.658 7.763 20928 Z= 0.312 Chirality : 0.044 0.255 2520 Planarity : 0.004 0.048 2490 Dihedral : 6.637 49.750 3657 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.21 % Allowed : 10.33 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1713 helix: 1.50 (0.28), residues: 369 sheet: 0.64 (0.25), residues: 441 loop : -0.52 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.016 0.001 TYR b 419 PHE 0.013 0.001 PHE A 117 TRP 0.030 0.001 TRP C 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00351 (15183) covalent geometry : angle 0.60701 (20607) SS BOND : bond 0.00376 ( 30) SS BOND : angle 1.74059 ( 60) hydrogen bonds : bond 0.03499 ( 561) hydrogen bonds : angle 4.77735 ( 1449) link_ALPHA1-2 : bond 0.00227 ( 3) link_ALPHA1-2 : angle 2.20973 ( 9) link_ALPHA1-3 : bond 0.01949 ( 6) link_ALPHA1-3 : angle 2.35624 ( 18) link_ALPHA1-6 : bond 0.00747 ( 6) link_ALPHA1-6 : angle 1.56169 ( 18) link_BETA1-4 : bond 0.00629 ( 36) link_BETA1-4 : angle 2.40517 ( 108) link_BETA1-6 : bond 0.00288 ( 3) link_BETA1-6 : angle 1.54341 ( 9) link_NAG-ASN : bond 0.00296 ( 33) link_NAG-ASN : angle 2.13314 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6901 (m170) cc_final: 0.6688 (m90) REVERT: A 151 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: A 204 ASP cc_start: 0.8544 (t0) cc_final: 0.8161 (t0) REVERT: B 115 HIS cc_start: 0.7210 (m170) cc_final: 0.6834 (m90) REVERT: B 151 GLU cc_start: 0.8109 (pt0) cc_final: 0.7734 (pm20) REVERT: C 185 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8392 (t0) REVERT: C 204 ASP cc_start: 0.8529 (t0) cc_final: 0.8320 (t0) REVERT: C 228 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8088 (mm-30) REVERT: J 123 LYS cc_start: 0.8546 (tttt) cc_final: 0.8228 (mttp) REVERT: L 123 LYS cc_start: 0.8442 (ttmm) cc_final: 0.8029 (mttm) REVERT: b 321 GLN cc_start: 0.8363 (mt0) cc_final: 0.8069 (mt0) REVERT: b 379 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8487 (mmm-85) REVERT: c 324 GLN cc_start: 0.8866 (mt0) cc_final: 0.8560 (mt0) REVERT: c 401 ASP cc_start: 0.8436 (m-30) cc_final: 0.8130 (m-30) REVERT: l 123 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8077 (mttm) outliers start: 34 outliers final: 28 residues processed: 208 average time/residue: 0.1356 time to fit residues: 41.5957 Evaluate side-chains 212 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 283 TRP Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076992 restraints weight = 27791.551| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.58 r_work: 0.3048 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15300 Z= 0.146 Angle : 0.661 8.081 20928 Z= 0.313 Chirality : 0.044 0.255 2520 Planarity : 0.004 0.050 2490 Dihedral : 6.485 51.719 3657 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.21 % Allowed : 10.07 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1713 helix: 1.52 (0.28), residues: 369 sheet: 0.71 (0.25), residues: 435 loop : -0.55 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.011 0.001 TYR h 38 PHE 0.013 0.001 PHE A 117 TRP 0.026 0.001 TRP A 210 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00342 (15183) covalent geometry : angle 0.61025 (20607) SS BOND : bond 0.00400 ( 30) SS BOND : angle 1.90205 ( 60) hydrogen bonds : bond 0.03439 ( 561) hydrogen bonds : angle 4.75350 ( 1449) link_ALPHA1-2 : bond 0.00256 ( 3) link_ALPHA1-2 : angle 2.22402 ( 9) link_ALPHA1-3 : bond 0.01864 ( 6) link_ALPHA1-3 : angle 2.28274 ( 18) link_ALPHA1-6 : bond 0.00769 ( 6) link_ALPHA1-6 : angle 1.53133 ( 18) link_BETA1-4 : bond 0.00626 ( 36) link_BETA1-4 : angle 2.35099 ( 108) link_BETA1-6 : bond 0.00267 ( 3) link_BETA1-6 : angle 1.57830 ( 9) link_NAG-ASN : bond 0.00288 ( 33) link_NAG-ASN : angle 2.12394 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6894 (m170) cc_final: 0.6672 (m90) REVERT: A 151 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: A 204 ASP cc_start: 0.8540 (t0) cc_final: 0.8205 (t0) REVERT: B 115 HIS cc_start: 0.7214 (m170) cc_final: 0.6829 (m90) REVERT: B 151 GLU cc_start: 0.8143 (pt0) cc_final: 0.7771 (pm20) REVERT: C 185 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 228 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8133 (mm-30) REVERT: J 123 LYS cc_start: 0.8546 (tttt) cc_final: 0.8229 (mttp) REVERT: L 123 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8016 (mttm) REVERT: b 321 GLN cc_start: 0.8384 (mt0) cc_final: 0.8075 (mt0) REVERT: b 379 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8486 (mmm-85) REVERT: c 324 GLN cc_start: 0.8877 (mt0) cc_final: 0.8614 (mt0) REVERT: c 332 MET cc_start: 0.8347 (tmt) cc_final: 0.7951 (tmt) REVERT: c 401 ASP cc_start: 0.8458 (m-30) cc_final: 0.8148 (m-30) REVERT: l 123 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8081 (mttm) outliers start: 34 outliers final: 28 residues processed: 211 average time/residue: 0.1345 time to fit residues: 41.6803 Evaluate side-chains 213 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 152 optimal weight: 0.0670 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.094885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076840 restraints weight = 27847.360| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.57 r_work: 0.3046 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15300 Z= 0.145 Angle : 0.657 8.974 20928 Z= 0.312 Chirality : 0.044 0.239 2520 Planarity : 0.005 0.051 2490 Dihedral : 6.368 53.528 3657 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 1.88 % Allowed : 10.66 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.32 (0.20), residues: 1713 helix: 1.56 (0.28), residues: 369 sheet: 0.70 (0.25), residues: 435 loop : -0.59 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 379 TYR 0.011 0.001 TYR h 38 PHE 0.013 0.001 PHE A 117 TRP 0.031 0.001 TRP C 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00341 (15183) covalent geometry : angle 0.60882 (20607) SS BOND : bond 0.00362 ( 30) SS BOND : angle 1.74161 ( 60) hydrogen bonds : bond 0.03433 ( 561) hydrogen bonds : angle 4.73769 ( 1449) link_ALPHA1-2 : bond 0.00268 ( 3) link_ALPHA1-2 : angle 2.23263 ( 9) link_ALPHA1-3 : bond 0.01805 ( 6) link_ALPHA1-3 : angle 2.21534 ( 18) link_ALPHA1-6 : bond 0.00783 ( 6) link_ALPHA1-6 : angle 1.49839 ( 18) link_BETA1-4 : bond 0.00620 ( 36) link_BETA1-4 : angle 2.30724 ( 108) link_BETA1-6 : bond 0.00254 ( 3) link_BETA1-6 : angle 1.60520 ( 9) link_NAG-ASN : bond 0.00286 ( 33) link_NAG-ASN : angle 2.11659 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6859 (m170) cc_final: 0.6619 (m90) REVERT: A 151 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7857 (pm20) REVERT: A 204 ASP cc_start: 0.8534 (t0) cc_final: 0.8184 (t0) REVERT: B 115 HIS cc_start: 0.7196 (m170) cc_final: 0.6824 (m90) REVERT: B 151 GLU cc_start: 0.8164 (pt0) cc_final: 0.7793 (pm20) REVERT: C 75 MET cc_start: 0.9197 (mtm) cc_final: 0.8816 (mtm) REVERT: C 185 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8224 (t0) REVERT: C 228 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8161 (mm-30) REVERT: I 81 ASP cc_start: 0.8025 (t0) cc_final: 0.7812 (t0) REVERT: J 123 LYS cc_start: 0.8542 (tttt) cc_final: 0.8223 (mttp) REVERT: L 123 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8007 (mttm) REVERT: b 321 GLN cc_start: 0.8373 (mt0) cc_final: 0.8066 (mt0) REVERT: b 379 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8479 (mmm-85) REVERT: c 324 GLN cc_start: 0.8889 (mt0) cc_final: 0.8603 (mt0) REVERT: c 332 MET cc_start: 0.8344 (tmt) cc_final: 0.7945 (tmt) REVERT: c 379 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8255 (mtp85) REVERT: c 401 ASP cc_start: 0.8465 (m-30) cc_final: 0.8160 (m-30) REVERT: l 123 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8109 (mttm) outliers start: 29 outliers final: 27 residues processed: 205 average time/residue: 0.1325 time to fit residues: 40.2586 Evaluate side-chains 213 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Chi-restraints excluded: chain l residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** 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 = 0.3490 r_free = 0.3490 target = 0.094987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076857 restraints weight = 27714.869| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.58 r_work: 0.3045 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15300 Z= 0.143 Angle : 0.659 10.200 20928 Z= 0.311 Chirality : 0.044 0.228 2520 Planarity : 0.005 0.054 2490 Dihedral : 6.266 55.180 3657 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.85 % Favored : 96.03 % Rotamer: Outliers : 1.95 % Allowed : 10.53 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.33 (0.20), residues: 1713 helix: 1.61 (0.28), residues: 369 sheet: 0.72 (0.25), residues: 435 loop : -0.61 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.011 0.001 TYR h 38 PHE 0.012 0.001 PHE A 117 TRP 0.036 0.001 TRP C 210 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00335 (15183) covalent geometry : angle 0.61338 (20607) SS BOND : bond 0.00357 ( 30) SS BOND : angle 1.64922 ( 60) hydrogen bonds : bond 0.03399 ( 561) hydrogen bonds : angle 4.71584 ( 1449) link_ALPHA1-2 : bond 0.00285 ( 3) link_ALPHA1-2 : angle 2.23827 ( 9) link_ALPHA1-3 : bond 0.01755 ( 6) link_ALPHA1-3 : angle 2.15906 ( 18) link_ALPHA1-6 : bond 0.00797 ( 6) link_ALPHA1-6 : angle 1.46663 ( 18) link_BETA1-4 : bond 0.00616 ( 36) link_BETA1-4 : angle 2.26550 ( 108) link_BETA1-6 : bond 0.00244 ( 3) link_BETA1-6 : angle 1.62168 ( 9) link_NAG-ASN : bond 0.00282 ( 33) link_NAG-ASN : angle 2.10299 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3426 Ramachandran restraints generated. 1713 Oldfield, 0 Emsley, 1713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 HIS cc_start: 0.6825 (m170) cc_final: 0.6596 (m90) REVERT: A 151 GLU cc_start: 0.8362 (pt0) cc_final: 0.7875 (pm20) REVERT: A 204 ASP cc_start: 0.8531 (t0) cc_final: 0.8160 (t0) REVERT: B 115 HIS cc_start: 0.7125 (m170) cc_final: 0.6759 (m90) REVERT: B 151 GLU cc_start: 0.8168 (pt0) cc_final: 0.7811 (pm20) REVERT: C 228 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8184 (mm-30) REVERT: J 123 LYS cc_start: 0.8574 (tttt) cc_final: 0.8264 (mttp) REVERT: L 123 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8005 (mttm) REVERT: b 312 MET cc_start: 0.8769 (mmm) cc_final: 0.8545 (mmm) REVERT: b 321 GLN cc_start: 0.8382 (mt0) cc_final: 0.8077 (mt0) REVERT: b 356 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8227 (mtt180) REVERT: b 379 ARG cc_start: 0.8713 (ttm-80) cc_final: 0.8498 (mmm-85) REVERT: b 420 MET cc_start: 0.8142 (mmp) cc_final: 0.7793 (tmm) REVERT: c 324 GLN cc_start: 0.8871 (mt0) cc_final: 0.8609 (mt0) REVERT: c 332 MET cc_start: 0.8276 (tmt) cc_final: 0.7930 (tmt) REVERT: c 379 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8263 (mtp85) REVERT: c 401 ASP cc_start: 0.8464 (m-30) cc_final: 0.8159 (m-30) REVERT: c 410 MET cc_start: 0.8508 (mtp) cc_final: 0.8236 (mtp) REVERT: l 3 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8431 (pt0) REVERT: l 123 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8112 (mttm) outliers start: 30 outliers final: 28 residues processed: 207 average time/residue: 0.1291 time to fit residues: 39.8774 Evaluate side-chains 212 residues out of total 1539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 85 ASN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain L residue 3 GLU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain a residue 360 CYS Chi-restraints excluded: chain b residue 284 MET Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 360 CYS Chi-restraints excluded: chain c residue 360 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 99 THR Chi-restraints excluded: chain h residue 101 VAL Chi-restraints excluded: chain l residue 3 GLU Chi-restraints excluded: chain l residue 97 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 319 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.093759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075595 restraints weight = 27828.427| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.58 r_work: 0.3022 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 15300 Z= 0.185 Angle : 0.684 10.254 20928 Z= 0.323 Chirality : 0.045 0.203 2520 Planarity : 0.005 0.055 2490 Dihedral : 6.300 58.034 3657 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 1.95 % Allowed : 10.79 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.28 (0.20), residues: 1713 helix: 1.54 (0.27), residues: 369 sheet: 0.90 (0.26), residues: 402 loop : -0.69 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 379 TYR 0.012 0.001 TYR h 38 PHE 0.016 0.001 PHE A 117 TRP 0.034 0.002 TRP C 210 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00445 (15183) covalent geometry : angle 0.63845 (20607) SS BOND : bond 0.00402 ( 30) SS BOND : angle 1.68787 ( 60) hydrogen bonds : bond 0.03582 ( 561) hydrogen bonds : angle 4.76203 ( 1449) link_ALPHA1-2 : bond 0.00366 ( 3) link_ALPHA1-2 : angle 2.27295 ( 9) link_ALPHA1-3 : bond 0.01697 ( 6) link_ALPHA1-3 : angle 2.10839 ( 18) link_ALPHA1-6 : bond 0.00758 ( 6) link_ALPHA1-6 : angle 1.46703 ( 18) link_BETA1-4 : bond 0.00602 ( 36) link_BETA1-4 : angle 2.28869 ( 108) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.68322 ( 9) link_NAG-ASN : bond 0.00316 ( 33) link_NAG-ASN : angle 2.18118 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3659.36 seconds wall clock time: 64 minutes 1.89 seconds (3841.89 seconds total)