Starting phenix.real_space_refine on Thu Mar 5 06:34:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.map" model { file = "/net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo1_21257/03_2026/6vo1_21257.cif" } resolution = 3.88 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= 0.073 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 123 5.16 5 C 12396 2.51 5 N 3300 2.21 5 O 3987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19806 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "E" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} 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: 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: "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: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: "a" 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: "b" 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: "c" 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: "d" 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: "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: 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: "g" 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: "h" 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: "i" 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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 Time building chain proxies: 5.04, per 1000 atoms: 0.25 Number of scatterers: 19806 At special positions: 0 Unit cell: (170.2, 166.75, 119.6, 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 123 16.00 O 3987 8.00 N 3300 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.15 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.15 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.15 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA Z 3 " - " MAN Z 6 " " BMA i 3 " - " MAN i 6 " BETA1-4 " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 618 " - " ASN A 295 " " NAG A 621 " - " ASN A 386 " " NAG A 626 " - " ASN A 355 " " NAG A 627 " - " ASN A 339 " " NAG A 628 " - " ASN A 133 " " NAG A 629 " - " ASN A 197 " " NAG C 618 " - " ASN C 295 " " NAG C 621 " - " ASN C 386 " " NAG C 626 " - " ASN C 355 " " NAG C 627 " - " ASN C 339 " " NAG C 628 " - " ASN C 133 " " NAG C 629 " - " ASN C 197 " " NAG D 618 " - " ASN D 295 " " NAG D 621 " - " ASN D 386 " " NAG D 626 " - " ASN D 355 " " NAG D 627 " - " ASN D 339 " " NAG D 628 " - " ASN D 133 " " NAG D 629 " - " ASN D 197 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN A 448 " " NAG V 1 " - " ASN C 88 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 392 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN D 88 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 160 " " NAG h 1 " - " ASN D 234 " " NAG i 1 " - " ASN D 262 " " NAG j 1 " - " ASN D 276 " " NAG k 1 " - " ASN D 332 " " NAG l 1 " - " ASN D 392 " " NAG m 1 " - " ASN D 448 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 970.7 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 22.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 560 through 565 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.581A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 560 through 565 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.095A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE H 48 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR H 59 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN H 50 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR H 57 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 48 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR G 59 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN G 50 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR G 57 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.073A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE I 48 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 59 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN I 50 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR I 57 " --> pdb=" O ASN I 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 1953 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: 4.60 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4204 1.32 - 1.45: 6292 1.45 - 1.58: 9547 1.58 - 1.72: 6 1.72 - 1.85: 156 Bond restraints: 20205 Sorted by residual: bond pdb=" CB TYR J 50 " pdb=" CG TYR J 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR L 50 " pdb=" CG TYR L 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR K 50 " pdb=" CG TYR K 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.64e+01 bond pdb=" CB TYR K 36 " pdb=" CG TYR K 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.60e+01 bond pdb=" CB TYR J 36 " pdb=" CG TYR J 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.59e+01 ... (remaining 20200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23734 2.53 - 5.07: 3191 5.07 - 7.60: 472 7.60 - 10.14: 38 10.14 - 12.67: 18 Bond angle restraints: 27453 Sorted by residual: angle pdb=" N SER F 613 " pdb=" CA SER F 613 " pdb=" C SER F 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER E 613 " pdb=" CA SER E 613 " pdb=" C SER E 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER B 613 " pdb=" CA SER B 613 " pdb=" C SER B 613 " ideal model delta sigma weight residual 114.62 101.97 12.65 1.14e+00 7.69e-01 1.23e+02 angle pdb=" N PHE D 53 " pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 111.36 122.40 -11.04 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 122.39 -11.03 1.09e+00 8.42e-01 1.02e+02 ... (remaining 27448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 12651 21.72 - 43.43: 375 43.43 - 65.15: 129 65.15 - 86.86: 51 86.86 - 108.58: 27 Dihedral angle restraints: 13233 sinusoidal: 6369 harmonic: 6864 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.29 -57.29 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.25 -57.25 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 13230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2574 0.113 - 0.226: 687 0.226 - 0.338: 87 0.338 - 0.451: 0 0.451 - 0.564: 6 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.33e+01 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 ... (remaining 3351 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.057 2.00e-02 2.50e+03 5.89e-02 4.34e+01 pdb=" CG ASN D 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.056 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" CG ASN C 392 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.056 2.00e-02 2.50e+03 5.87e-02 4.30e+01 pdb=" CG ASN A 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.070 2.00e-02 2.50e+03 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 335 2.61 - 3.18: 17911 3.18 - 3.75: 31236 3.75 - 4.33: 45173 4.33 - 4.90: 70376 Nonbonded interactions: 165031 Sorted by model distance: nonbonded pdb=" CZ PHE A 288 " pdb=" CD1 LEU A 452 " model vdw 2.033 3.760 nonbonded pdb=" CZ PHE C 288 " pdb=" CD1 LEU C 452 " model vdw 2.034 3.760 nonbonded pdb=" CZ PHE D 288 " pdb=" CD1 LEU D 452 " model vdw 2.035 3.760 nonbonded pdb=" OG1 THR A 357 " pdb=" OG1 THR A 465 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR C 357 " pdb=" OG1 THR C 465 " model vdw 2.314 3.040 ... (remaining 165026 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'Z' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.110 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.020 0.123 20334 Z= 1.106 Angle : 1.829 12.674 27798 Z= 1.161 Chirality : 0.101 0.564 3354 Planarity : 0.009 0.049 3366 Dihedral : 13.289 108.579 8679 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 1.29 % Allowed : 4.50 % Favored : 94.22 % Rotamer: Outliers : 0.72 % Allowed : 0.57 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: 0.04 (0.17), residues: 2334 helix: -0.19 (0.23), residues: 453 sheet: 0.58 (0.19), residues: 681 loop : -0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.045 0.010 TYR J 36 PHE 0.032 0.006 PHE I 78 TRP 0.054 0.010 TRP J 35 HIS 0.017 0.003 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02035 (20205) covalent geometry : angle 1.80948 (27453) SS BOND : bond 0.03266 ( 42) SS BOND : angle 2.62598 ( 84) hydrogen bonds : bond 0.15268 ( 750) hydrogen bonds : angle 7.79749 ( 1953) link_ALPHA1-2 : bond 0.04223 ( 3) link_ALPHA1-2 : angle 2.80402 ( 9) link_ALPHA1-3 : bond 0.03065 ( 3) link_ALPHA1-3 : angle 2.37911 ( 9) link_ALPHA1-6 : bond 0.03640 ( 3) link_ALPHA1-6 : angle 3.23554 ( 9) link_BETA1-4 : bond 0.02857 ( 33) link_BETA1-4 : angle 3.93956 ( 99) link_NAG-ASN : bond 0.02673 ( 45) link_NAG-ASN : angle 2.45750 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 418 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8770 (mmm) cc_final: 0.8451 (mmt) REVERT: B 539 VAL cc_start: 0.9160 (t) cc_final: 0.8612 (t) REVERT: B 588 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8216 (mtt180) REVERT: L 93 ASN cc_start: 0.9074 (t0) cc_final: 0.8804 (m110) REVERT: E 539 VAL cc_start: 0.9198 (t) cc_final: 0.8770 (t) REVERT: E 586 TYR cc_start: 0.9305 (t80) cc_final: 0.9053 (t80) REVERT: E 588 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8168 (mtt180) REVERT: D 112 TRP cc_start: 0.8410 (t-100) cc_final: 0.8034 (t-100) REVERT: D 150 MET cc_start: 0.8793 (mmm) cc_final: 0.8580 (mmp) REVERT: F 588 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8112 (mtt180) REVERT: K 93 ASN cc_start: 0.9048 (t0) cc_final: 0.8830 (m-40) outliers start: 15 outliers final: 9 residues processed: 433 average time/residue: 0.1694 time to fit residues: 108.5617 Evaluate side-chains 191 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 91 HIS C 352 HIS ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN J 53 ASN J 91 HIS J 92 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.058784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048012 restraints weight = 100333.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049849 restraints weight = 48891.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051111 restraints weight = 31107.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051933 restraints weight = 22906.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.052536 restraints weight = 18562.855| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20334 Z= 0.197 Angle : 0.870 12.901 27798 Z= 0.433 Chirality : 0.048 0.227 3354 Planarity : 0.004 0.030 3366 Dihedral : 9.852 80.931 4344 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.18 % Favored : 94.17 % Rotamer: Outliers : 1.77 % Allowed : 7.84 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.25 (0.17), residues: 2334 helix: 0.19 (0.24), residues: 471 sheet: 0.53 (0.20), residues: 675 loop : -0.68 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 65 TYR 0.017 0.002 TYR J 50 PHE 0.018 0.002 PHE G 78 TRP 0.039 0.002 TRP B 628 HIS 0.008 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00427 (20205) covalent geometry : angle 0.83133 (27453) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.08708 ( 84) hydrogen bonds : bond 0.05554 ( 750) hydrogen bonds : angle 6.05540 ( 1953) link_ALPHA1-2 : bond 0.00195 ( 3) link_ALPHA1-2 : angle 1.44746 ( 9) link_ALPHA1-3 : bond 0.01608 ( 3) link_ALPHA1-3 : angle 2.64336 ( 9) link_ALPHA1-6 : bond 0.00225 ( 3) link_ALPHA1-6 : angle 1.44475 ( 9) link_BETA1-4 : bond 0.00455 ( 33) link_BETA1-4 : angle 2.68633 ( 99) link_NAG-ASN : bond 0.00300 ( 45) link_NAG-ASN : angle 2.94750 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 MET cc_start: 0.7854 (mmm) cc_final: 0.7638 (mmm) REVERT: A 427 TRP cc_start: 0.8350 (m-90) cc_final: 0.7890 (m-10) REVERT: B 571 TRP cc_start: 0.8599 (m100) cc_final: 0.8280 (m100) REVERT: B 626 MET cc_start: 0.7659 (ttm) cc_final: 0.5907 (mtp) REVERT: H 65 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8540 (mmm160) REVERT: L 70 ASP cc_start: 0.8830 (m-30) cc_final: 0.8196 (p0) REVERT: L 93 ASN cc_start: 0.9107 (t0) cc_final: 0.8803 (m110) REVERT: C 104 MET cc_start: 0.9252 (ttm) cc_final: 0.8978 (ttm) REVERT: C 150 MET cc_start: 0.8536 (mmt) cc_final: 0.8297 (mtp) REVERT: C 427 TRP cc_start: 0.8426 (m-90) cc_final: 0.7758 (m-10) REVERT: E 626 MET cc_start: 0.7695 (ttm) cc_final: 0.6829 (mtp) REVERT: E 647 GLU cc_start: 0.8814 (pp20) cc_final: 0.8568 (tm-30) REVERT: G 72 ASP cc_start: 0.8290 (t0) cc_final: 0.8058 (t0) REVERT: D 161 MET cc_start: 0.8547 (tpt) cc_final: 0.7899 (tpt) REVERT: D 381 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: F 656 ASN cc_start: 0.9600 (m-40) cc_final: 0.9364 (m-40) REVERT: I 33 TYR cc_start: 0.8463 (m-80) cc_final: 0.8197 (m-80) REVERT: K 49 TYR cc_start: 0.9049 (p90) cc_final: 0.8762 (p90) REVERT: K 89 GLN cc_start: 0.8510 (pp30) cc_final: 0.7880 (tm-30) REVERT: K 93 ASN cc_start: 0.9101 (t0) cc_final: 0.8772 (m110) outliers start: 37 outliers final: 17 residues processed: 284 average time/residue: 0.1570 time to fit residues: 66.7765 Evaluate side-chains 199 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 230 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 161 optimal weight: 0.4980 chunk 87 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 89 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 105 GLN J 89 GLN D 114 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS K 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047616 restraints weight = 102916.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049425 restraints weight = 48967.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.050649 restraints weight = 30467.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051436 restraints weight = 22065.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051991 restraints weight = 17734.034| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20334 Z= 0.157 Angle : 0.771 13.388 27798 Z= 0.374 Chirality : 0.046 0.290 3354 Planarity : 0.004 0.037 3366 Dihedral : 8.112 72.006 4336 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.36 % Favored : 94.13 % Rotamer: Outliers : 1.82 % Allowed : 9.18 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.18 (0.17), residues: 2334 helix: 0.74 (0.25), residues: 456 sheet: 0.49 (0.20), residues: 672 loop : -0.78 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 65 TYR 0.026 0.002 TYR K 50 PHE 0.018 0.002 PHE D 210 TRP 0.035 0.002 TRP F 571 HIS 0.009 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00339 (20205) covalent geometry : angle 0.73530 (27453) SS BOND : bond 0.00357 ( 42) SS BOND : angle 0.86373 ( 84) hydrogen bonds : bond 0.04683 ( 750) hydrogen bonds : angle 5.59816 ( 1953) link_ALPHA1-2 : bond 0.00287 ( 3) link_ALPHA1-2 : angle 1.37131 ( 9) link_ALPHA1-3 : bond 0.01547 ( 3) link_ALPHA1-3 : angle 1.36854 ( 9) link_ALPHA1-6 : bond 0.00786 ( 3) link_ALPHA1-6 : angle 1.81851 ( 9) link_BETA1-4 : bond 0.00384 ( 33) link_BETA1-4 : angle 2.38299 ( 99) link_NAG-ASN : bond 0.00309 ( 45) link_NAG-ASN : angle 2.69294 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9021 (ttm) REVERT: A 434 MET cc_start: 0.6943 (mmm) cc_final: 0.6607 (mmt) REVERT: B 574 LYS cc_start: 0.9266 (mtmt) cc_final: 0.9011 (mtmm) REVERT: B 584 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 586 TYR cc_start: 0.8568 (t80) cc_final: 0.8257 (t80) REVERT: B 589 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7829 (p0) REVERT: H 46 GLU cc_start: 0.8325 (mp0) cc_final: 0.7960 (mp0) REVERT: L 70 ASP cc_start: 0.8715 (m-30) cc_final: 0.7989 (p0) REVERT: L 89 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: L 93 ASN cc_start: 0.9137 (t0) cc_final: 0.8812 (m-40) REVERT: C 104 MET cc_start: 0.9263 (ttm) cc_final: 0.8882 (ttm) REVERT: C 427 TRP cc_start: 0.8222 (m-90) cc_final: 0.7942 (m-10) REVERT: E 574 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9018 (pttm) REVERT: E 584 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8581 (tm-30) REVERT: J 89 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: D 112 TRP cc_start: 0.8509 (t-100) cc_final: 0.8113 (t-100) REVERT: D 122 LEU cc_start: 0.9287 (mt) cc_final: 0.9041 (pp) REVERT: D 381 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: F 656 ASN cc_start: 0.9560 (m-40) cc_final: 0.9317 (m-40) REVERT: I 29 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8936 (mm) REVERT: K 49 TYR cc_start: 0.9210 (p90) cc_final: 0.8885 (p90) REVERT: K 93 ASN cc_start: 0.9155 (t0) cc_final: 0.8840 (m-40) REVERT: K 103 LYS cc_start: 0.9085 (tptm) cc_final: 0.8869 (tptp) outliers start: 38 outliers final: 16 residues processed: 228 average time/residue: 0.1503 time to fit residues: 51.9669 Evaluate side-chains 194 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 567 LYS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 126 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.055592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044120 restraints weight = 103076.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045828 restraints weight = 50856.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.046992 restraints weight = 32980.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047784 restraints weight = 24898.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048291 restraints weight = 20420.163| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 20334 Z= 0.201 Angle : 0.744 9.615 27798 Z= 0.360 Chirality : 0.045 0.283 3354 Planarity : 0.004 0.064 3366 Dihedral : 7.140 60.116 4336 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.66 % Favored : 93.92 % Rotamer: Outliers : 2.01 % Allowed : 9.18 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.14 (0.17), residues: 2334 helix: 0.78 (0.26), residues: 459 sheet: 0.55 (0.20), residues: 657 loop : -0.77 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 65 TYR 0.028 0.002 TYR L 50 PHE 0.016 0.002 PHE I 78 TRP 0.036 0.002 TRP E 571 HIS 0.012 0.002 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00446 (20205) covalent geometry : angle 0.70892 (27453) SS BOND : bond 0.00412 ( 42) SS BOND : angle 0.77716 ( 84) hydrogen bonds : bond 0.04330 ( 750) hydrogen bonds : angle 5.33020 ( 1953) link_ALPHA1-2 : bond 0.00141 ( 3) link_ALPHA1-2 : angle 1.55939 ( 9) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.70891 ( 9) link_ALPHA1-6 : bond 0.00865 ( 3) link_ALPHA1-6 : angle 1.67781 ( 9) link_BETA1-4 : bond 0.00264 ( 33) link_BETA1-4 : angle 2.22312 ( 99) link_NAG-ASN : bond 0.00482 ( 45) link_NAG-ASN : angle 2.69068 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9427 (ptm) cc_final: 0.9205 (ppp) REVERT: A 104 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9085 (ttm) REVERT: A 161 MET cc_start: 0.8144 (tpt) cc_final: 0.7907 (tpt) REVERT: A 434 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6562 (mmt) REVERT: A 465 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (m) REVERT: B 584 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 626 MET cc_start: 0.7830 (mtp) cc_final: 0.7322 (ttt) REVERT: H 46 GLU cc_start: 0.8231 (mp0) cc_final: 0.7916 (mp0) REVERT: L 70 ASP cc_start: 0.8673 (m-30) cc_final: 0.8008 (p0) REVERT: L 93 ASN cc_start: 0.9093 (t0) cc_final: 0.8785 (m-40) REVERT: C 104 MET cc_start: 0.9310 (ttm) cc_final: 0.8904 (ttm) REVERT: C 465 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8139 (m) REVERT: E 566 LEU cc_start: 0.9338 (mt) cc_final: 0.9013 (pp) REVERT: E 584 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8573 (tm-30) REVERT: E 626 MET cc_start: 0.8468 (mtp) cc_final: 0.7945 (ttt) REVERT: D 95 MET cc_start: 0.9390 (ptm) cc_final: 0.9111 (ppp) REVERT: D 104 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8971 (ttm) REVERT: D 112 TRP cc_start: 0.8686 (t-100) cc_final: 0.8381 (t-100) REVERT: D 115 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.9088 (p) REVERT: D 150 MET cc_start: 0.9126 (mmp) cc_final: 0.8831 (mmt) REVERT: D 381 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 426 MET cc_start: 0.8427 (mmm) cc_final: 0.8179 (tpp) REVERT: D 465 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8117 (m) REVERT: F 566 LEU cc_start: 0.9198 (mt) cc_final: 0.8836 (pp) REVERT: F 656 ASN cc_start: 0.9511 (m-40) cc_final: 0.9286 (m110) REVERT: I 29 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8806 (mm) REVERT: K 49 TYR cc_start: 0.9328 (p90) cc_final: 0.8901 (p90) REVERT: K 93 ASN cc_start: 0.9147 (t0) cc_final: 0.8925 (m-40) REVERT: K 103 LYS cc_start: 0.9154 (tptm) cc_final: 0.8938 (tptp) outliers start: 42 outliers final: 20 residues processed: 214 average time/residue: 0.1459 time to fit residues: 48.5801 Evaluate side-chains 191 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 105 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN J 89 GLN I 76 ASN K 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041592 restraints weight = 105960.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043239 restraints weight = 54203.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044311 restraints weight = 35813.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.045051 restraints weight = 27402.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045526 restraints weight = 22876.788| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 20334 Z= 0.314 Angle : 0.823 9.941 27798 Z= 0.400 Chirality : 0.047 0.425 3354 Planarity : 0.005 0.083 3366 Dihedral : 6.952 56.330 4336 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.00 % Favored : 93.40 % Rotamer: Outliers : 1.96 % Allowed : 10.28 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.42 (0.17), residues: 2334 helix: 0.59 (0.25), residues: 465 sheet: 0.38 (0.20), residues: 654 loop : -0.98 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 65 TYR 0.024 0.002 TYR B 643 PHE 0.017 0.002 PHE G 78 TRP 0.035 0.002 TRP E 571 HIS 0.010 0.002 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00698 (20205) covalent geometry : angle 0.78986 (27453) SS BOND : bond 0.00588 ( 42) SS BOND : angle 0.90482 ( 84) hydrogen bonds : bond 0.04632 ( 750) hydrogen bonds : angle 5.49568 ( 1953) link_ALPHA1-2 : bond 0.00056 ( 3) link_ALPHA1-2 : angle 1.66679 ( 9) link_ALPHA1-3 : bond 0.00597 ( 3) link_ALPHA1-3 : angle 1.66132 ( 9) link_ALPHA1-6 : bond 0.00672 ( 3) link_ALPHA1-6 : angle 1.33447 ( 9) link_BETA1-4 : bond 0.00294 ( 33) link_BETA1-4 : angle 2.23804 ( 99) link_NAG-ASN : bond 0.00756 ( 45) link_NAG-ASN : angle 2.82693 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.9065 (ttm) REVERT: A 161 MET cc_start: 0.8050 (tpt) cc_final: 0.7834 (tpt) REVERT: A 465 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8186 (m) REVERT: B 530 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: B 566 LEU cc_start: 0.9200 (mt) cc_final: 0.8819 (pp) REVERT: B 574 LYS cc_start: 0.9536 (mtmm) cc_final: 0.9051 (mtmm) REVERT: B 584 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 626 MET cc_start: 0.8305 (mtp) cc_final: 0.7513 (ttt) REVERT: L 93 ASN cc_start: 0.9142 (t0) cc_final: 0.8771 (m-40) REVERT: C 104 MET cc_start: 0.9341 (ttm) cc_final: 0.8997 (ttm) REVERT: E 566 LEU cc_start: 0.9319 (mt) cc_final: 0.8985 (pp) REVERT: E 584 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8524 (tm-30) REVERT: E 626 MET cc_start: 0.8598 (mtp) cc_final: 0.7920 (ttt) REVERT: E 643 TYR cc_start: 0.9030 (m-10) cc_final: 0.8756 (m-80) REVERT: G 33 TYR cc_start: 0.8393 (m-80) cc_final: 0.8100 (m-80) REVERT: J 3 VAL cc_start: 0.9391 (t) cc_final: 0.9183 (p) REVERT: J 4 MET cc_start: 0.8032 (mmm) cc_final: 0.7487 (mmm) REVERT: J 103 LYS cc_start: 0.9043 (tptm) cc_final: 0.8813 (tptp) REVERT: D 150 MET cc_start: 0.9151 (mmp) cc_final: 0.8910 (mmt) REVERT: D 381 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: D 465 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8273 (m) REVERT: F 530 MET cc_start: 0.8657 (mtm) cc_final: 0.8194 (mmm) REVERT: F 566 LEU cc_start: 0.9190 (mt) cc_final: 0.8834 (pp) REVERT: F 656 ASN cc_start: 0.9470 (m-40) cc_final: 0.9257 (m110) REVERT: I 29 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8727 (mm) REVERT: K 49 TYR cc_start: 0.9444 (p90) cc_final: 0.9056 (p90) REVERT: K 93 ASN cc_start: 0.9181 (t0) cc_final: 0.8980 (m-40) REVERT: K 103 LYS cc_start: 0.9172 (tptm) cc_final: 0.8941 (tptp) outliers start: 41 outliers final: 20 residues processed: 197 average time/residue: 0.1467 time to fit residues: 44.9600 Evaluate side-chains 170 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 87 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.054410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.042820 restraints weight = 103703.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044510 restraints weight = 51949.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.045624 restraints weight = 33850.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046390 restraints weight = 25644.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046834 restraints weight = 21247.160| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20334 Z= 0.160 Angle : 0.704 9.711 27798 Z= 0.341 Chirality : 0.045 0.345 3354 Planarity : 0.004 0.058 3366 Dihedral : 6.352 59.908 4326 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.66 % Favored : 93.83 % Rotamer: Outliers : 1.63 % Allowed : 10.81 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.39 (0.17), residues: 2334 helix: 0.70 (0.25), residues: 465 sheet: 0.41 (0.20), residues: 684 loop : -1.04 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 65 TYR 0.040 0.002 TYR B 643 PHE 0.013 0.001 PHE G 78 TRP 0.045 0.002 TRP B 571 HIS 0.010 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00352 (20205) covalent geometry : angle 0.67303 (27453) SS BOND : bond 0.00325 ( 42) SS BOND : angle 0.69712 ( 84) hydrogen bonds : bond 0.03991 ( 750) hydrogen bonds : angle 5.18217 ( 1953) link_ALPHA1-2 : bond 0.00135 ( 3) link_ALPHA1-2 : angle 1.62370 ( 9) link_ALPHA1-3 : bond 0.01084 ( 3) link_ALPHA1-3 : angle 1.28210 ( 9) link_ALPHA1-6 : bond 0.00685 ( 3) link_ALPHA1-6 : angle 1.33847 ( 9) link_BETA1-4 : bond 0.00300 ( 33) link_BETA1-4 : angle 2.05206 ( 99) link_NAG-ASN : bond 0.00482 ( 45) link_NAG-ASN : angle 2.47876 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9097 (ttm) REVERT: A 271 MET cc_start: 0.8258 (mmm) cc_final: 0.7939 (mmm) REVERT: B 530 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7703 (mmm) REVERT: B 566 LEU cc_start: 0.9192 (mt) cc_final: 0.8827 (pp) REVERT: B 574 LYS cc_start: 0.9502 (mtmm) cc_final: 0.8874 (mtmm) REVERT: B 584 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 626 MET cc_start: 0.8228 (mtp) cc_final: 0.7565 (ttt) REVERT: L 93 ASN cc_start: 0.9061 (t0) cc_final: 0.8734 (m-40) REVERT: C 53 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8158 (m-10) REVERT: C 104 MET cc_start: 0.9353 (ttm) cc_final: 0.8959 (ttm) REVERT: E 530 MET cc_start: 0.8498 (mmm) cc_final: 0.8284 (mmm) REVERT: E 566 LEU cc_start: 0.9275 (mt) cc_final: 0.8923 (pp) REVERT: E 584 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 626 MET cc_start: 0.8514 (mtp) cc_final: 0.8055 (ttt) REVERT: E 643 TYR cc_start: 0.9059 (m-10) cc_final: 0.8774 (m-80) REVERT: G 65 ARG cc_start: 0.8711 (mmm160) cc_final: 0.8464 (mmm160) REVERT: G 102 TYR cc_start: 0.8980 (m-80) cc_final: 0.8668 (m-10) REVERT: J 4 MET cc_start: 0.8062 (mmm) cc_final: 0.7706 (mmm) REVERT: J 103 LYS cc_start: 0.9039 (tptm) cc_final: 0.8812 (tptp) REVERT: D 104 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8788 (ttm) REVERT: D 381 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: D 465 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8172 (m) REVERT: F 566 LEU cc_start: 0.9140 (mt) cc_final: 0.8782 (pp) REVERT: F 574 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8812 (pttm) REVERT: F 626 MET cc_start: 0.8429 (ttm) cc_final: 0.8159 (ttm) REVERT: F 656 ASN cc_start: 0.9488 (m-40) cc_final: 0.9257 (m110) REVERT: I 29 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8683 (mm) REVERT: K 49 TYR cc_start: 0.9348 (p90) cc_final: 0.9031 (p90) REVERT: K 93 ASN cc_start: 0.9156 (t0) cc_final: 0.8889 (m-40) REVERT: K 103 LYS cc_start: 0.9175 (tptm) cc_final: 0.8940 (tptp) outliers start: 34 outliers final: 19 residues processed: 191 average time/residue: 0.1476 time to fit residues: 43.3816 Evaluate side-chains 178 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** D 195 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 = 0.3192 r_free = 0.3192 target = 0.052796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041201 restraints weight = 108862.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.042809 restraints weight = 55639.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043911 restraints weight = 36764.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044605 restraints weight = 28069.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045091 restraints weight = 23562.632| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20334 Z= 0.281 Angle : 0.776 10.146 27798 Z= 0.378 Chirality : 0.046 0.353 3354 Planarity : 0.005 0.082 3366 Dihedral : 6.280 54.248 4326 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.43 % Favored : 92.97 % Rotamer: Outliers : 1.72 % Allowed : 11.24 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.17), residues: 2334 helix: 0.50 (0.25), residues: 465 sheet: 0.45 (0.21), residues: 657 loop : -1.18 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 65 TYR 0.048 0.002 TYR B 643 PHE 0.016 0.002 PHE G 78 TRP 0.045 0.002 TRP F 571 HIS 0.008 0.002 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00624 (20205) covalent geometry : angle 0.74601 (27453) SS BOND : bond 0.00517 ( 42) SS BOND : angle 0.80921 ( 84) hydrogen bonds : bond 0.04359 ( 750) hydrogen bonds : angle 5.32786 ( 1953) link_ALPHA1-2 : bond 0.00043 ( 3) link_ALPHA1-2 : angle 1.71953 ( 9) link_ALPHA1-3 : bond 0.00639 ( 3) link_ALPHA1-3 : angle 1.38281 ( 9) link_ALPHA1-6 : bond 0.00424 ( 3) link_ALPHA1-6 : angle 1.45021 ( 9) link_BETA1-4 : bond 0.00294 ( 33) link_BETA1-4 : angle 2.13880 ( 99) link_NAG-ASN : bond 0.00729 ( 45) link_NAG-ASN : angle 2.55078 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: A 104 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9060 (ttm) REVERT: B 566 LEU cc_start: 0.9175 (mt) cc_final: 0.8804 (pp) REVERT: B 574 LYS cc_start: 0.9503 (mtmm) cc_final: 0.8925 (mtmm) REVERT: B 584 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 586 TYR cc_start: 0.8728 (t80) cc_final: 0.8509 (t80) REVERT: L 3 VAL cc_start: 0.9373 (t) cc_final: 0.9106 (p) REVERT: L 93 ASN cc_start: 0.9084 (t0) cc_final: 0.8756 (m-40) REVERT: C 53 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8242 (m-10) REVERT: C 95 MET cc_start: 0.9432 (ptm) cc_final: 0.9055 (ppp) REVERT: C 104 MET cc_start: 0.9368 (ttm) cc_final: 0.9005 (ttm) REVERT: E 530 MET cc_start: 0.8785 (mmm) cc_final: 0.8332 (mmm) REVERT: E 566 LEU cc_start: 0.9268 (mt) cc_final: 0.8940 (pp) REVERT: E 574 LYS cc_start: 0.9290 (mtmm) cc_final: 0.9036 (mtmm) REVERT: E 584 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8523 (tm-30) REVERT: G 65 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8630 (mmm160) REVERT: G 75 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9240 (mmmt) REVERT: J 103 LYS cc_start: 0.9052 (tptm) cc_final: 0.8815 (tptp) REVERT: D 104 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8842 (ttm) REVERT: D 381 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: D 465 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (m) REVERT: F 566 LEU cc_start: 0.9129 (mt) cc_final: 0.8775 (pp) REVERT: F 584 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 656 ASN cc_start: 0.9467 (m-40) cc_final: 0.9253 (m110) REVERT: K 49 TYR cc_start: 0.9452 (p90) cc_final: 0.9126 (p90) REVERT: K 93 ASN cc_start: 0.9163 (t0) cc_final: 0.8873 (t0) REVERT: K 103 LYS cc_start: 0.9189 (tptm) cc_final: 0.8943 (tptp) outliers start: 36 outliers final: 20 residues processed: 170 average time/residue: 0.1421 time to fit residues: 37.5261 Evaluate side-chains 172 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN J 89 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.053631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042069 restraints weight = 107779.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043713 restraints weight = 54801.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044798 restraints weight = 36052.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045550 restraints weight = 27537.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.046019 restraints weight = 22888.893| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20334 Z= 0.181 Angle : 0.712 11.634 27798 Z= 0.346 Chirality : 0.045 0.334 3354 Planarity : 0.004 0.058 3366 Dihedral : 5.820 43.211 4326 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.08 % Favored : 93.23 % Rotamer: Outliers : 1.63 % Allowed : 11.43 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.56 (0.17), residues: 2334 helix: 0.60 (0.25), residues: 462 sheet: 0.53 (0.22), residues: 615 loop : -1.24 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 65 TYR 0.053 0.002 TYR E 643 PHE 0.013 0.001 PHE G 78 TRP 0.045 0.002 TRP F 571 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00404 (20205) covalent geometry : angle 0.68476 (27453) SS BOND : bond 0.00340 ( 42) SS BOND : angle 0.67525 ( 84) hydrogen bonds : bond 0.03986 ( 750) hydrogen bonds : angle 5.14310 ( 1953) link_ALPHA1-2 : bond 0.00080 ( 3) link_ALPHA1-2 : angle 1.64864 ( 9) link_ALPHA1-3 : bond 0.00752 ( 3) link_ALPHA1-3 : angle 1.03010 ( 9) link_ALPHA1-6 : bond 0.00289 ( 3) link_ALPHA1-6 : angle 1.54046 ( 9) link_BETA1-4 : bond 0.00275 ( 33) link_BETA1-4 : angle 2.01187 ( 99) link_NAG-ASN : bond 0.00523 ( 45) link_NAG-ASN : angle 2.32816 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: A 104 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9090 (ttm) REVERT: A 426 MET cc_start: 0.8479 (ttm) cc_final: 0.8257 (ttm) REVERT: B 566 LEU cc_start: 0.9175 (mt) cc_final: 0.8787 (pp) REVERT: B 574 LYS cc_start: 0.9489 (mtmm) cc_final: 0.8876 (mtmm) REVERT: B 584 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 626 MET cc_start: 0.8344 (mtp) cc_final: 0.7901 (ttt) REVERT: L 3 VAL cc_start: 0.9384 (t) cc_final: 0.9131 (p) REVERT: L 93 ASN cc_start: 0.9036 (t0) cc_final: 0.8778 (t0) REVERT: C 53 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: C 104 MET cc_start: 0.9368 (ttm) cc_final: 0.8957 (ttm) REVERT: C 426 MET cc_start: 0.8710 (ttm) cc_final: 0.8487 (ttm) REVERT: E 530 MET cc_start: 0.8642 (mmm) cc_final: 0.8286 (mmm) REVERT: E 566 LEU cc_start: 0.9252 (mt) cc_final: 0.8903 (pp) REVERT: E 574 LYS cc_start: 0.9250 (mtmm) cc_final: 0.8956 (mtmm) REVERT: E 584 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8537 (tm-30) REVERT: E 626 MET cc_start: 0.8565 (mtp) cc_final: 0.8070 (ttt) REVERT: J 103 LYS cc_start: 0.9047 (tptm) cc_final: 0.8809 (tptp) REVERT: D 104 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8833 (ttm) REVERT: D 381 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: D 465 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8188 (m) REVERT: F 566 LEU cc_start: 0.9154 (mt) cc_final: 0.8803 (pp) REVERT: F 574 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8784 (pttm) REVERT: F 584 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8557 (tm-30) REVERT: F 656 ASN cc_start: 0.9478 (m-40) cc_final: 0.9257 (m110) REVERT: K 3 VAL cc_start: 0.9341 (t) cc_final: 0.9131 (p) REVERT: K 49 TYR cc_start: 0.9420 (p90) cc_final: 0.9111 (p90) REVERT: K 93 ASN cc_start: 0.9101 (t0) cc_final: 0.8838 (t0) REVERT: K 97 THR cc_start: 0.8920 (m) cc_final: 0.8141 (p) REVERT: K 103 LYS cc_start: 0.9181 (tptm) cc_final: 0.8931 (tptp) outliers start: 34 outliers final: 21 residues processed: 185 average time/residue: 0.1445 time to fit residues: 41.2247 Evaluate side-chains 175 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN J 89 GLN ** D 195 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 = 0.3212 r_free = 0.3212 target = 0.053656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042088 restraints weight = 108122.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.043709 restraints weight = 55136.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044806 restraints weight = 36316.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045533 restraints weight = 27791.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046019 restraints weight = 23176.726| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20334 Z= 0.191 Angle : 0.726 11.710 27798 Z= 0.352 Chirality : 0.045 0.329 3354 Planarity : 0.004 0.072 3366 Dihedral : 5.691 40.035 4326 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.17 % Favored : 93.10 % Rotamer: Outliers : 1.67 % Allowed : 11.72 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 (0.17), residues: 2334 helix: 0.50 (0.25), residues: 462 sheet: 0.51 (0.22), residues: 618 loop : -1.28 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 65 TYR 0.069 0.002 TYR E 643 PHE 0.014 0.001 PHE H 78 TRP 0.081 0.002 TRP F 571 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00428 (20205) covalent geometry : angle 0.70049 (27453) SS BOND : bond 0.00352 ( 42) SS BOND : angle 0.71921 ( 84) hydrogen bonds : bond 0.04055 ( 750) hydrogen bonds : angle 5.14783 ( 1953) link_ALPHA1-2 : bond 0.00091 ( 3) link_ALPHA1-2 : angle 1.64431 ( 9) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 1.15240 ( 9) link_ALPHA1-6 : bond 0.00453 ( 3) link_ALPHA1-6 : angle 1.53153 ( 9) link_BETA1-4 : bond 0.00249 ( 33) link_BETA1-4 : angle 2.00379 ( 99) link_NAG-ASN : bond 0.00522 ( 45) link_NAG-ASN : angle 2.26390 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: A 104 MET cc_start: 0.9379 (ttm) cc_final: 0.9065 (ttm) REVERT: B 566 LEU cc_start: 0.9176 (mt) cc_final: 0.8834 (pp) REVERT: B 574 LYS cc_start: 0.9470 (mtmm) cc_final: 0.8846 (mtmm) REVERT: B 584 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 626 MET cc_start: 0.8376 (mtp) cc_final: 0.7850 (ttt) REVERT: B 639 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 643 TYR cc_start: 0.9000 (m-80) cc_final: 0.8654 (m-80) REVERT: H 65 ARG cc_start: 0.8820 (mmm160) cc_final: 0.8620 (mmm160) REVERT: L 3 VAL cc_start: 0.9390 (t) cc_final: 0.9137 (p) REVERT: L 93 ASN cc_start: 0.9069 (t0) cc_final: 0.8812 (t0) REVERT: C 53 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8216 (m-10) REVERT: C 104 MET cc_start: 0.9390 (ttm) cc_final: 0.8987 (ttm) REVERT: E 530 MET cc_start: 0.8736 (mmm) cc_final: 0.8276 (mmm) REVERT: E 566 LEU cc_start: 0.9242 (mt) cc_final: 0.8839 (pp) REVERT: E 574 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8951 (mtmm) REVERT: E 584 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8535 (tm-30) REVERT: E 626 MET cc_start: 0.8624 (mtp) cc_final: 0.7950 (ttt) REVERT: E 643 TYR cc_start: 0.9032 (m-80) cc_final: 0.8798 (m-80) REVERT: J 103 LYS cc_start: 0.9044 (tptm) cc_final: 0.8800 (tptp) REVERT: D 104 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8836 (ttm) REVERT: D 426 MET cc_start: 0.8331 (ttm) cc_final: 0.8108 (ttm) REVERT: D 465 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (m) REVERT: F 530 MET cc_start: 0.8328 (mmm) cc_final: 0.8115 (mmm) REVERT: F 566 LEU cc_start: 0.9137 (mt) cc_final: 0.8796 (pp) REVERT: F 574 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8867 (mtmm) REVERT: F 584 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8547 (tm-30) REVERT: F 656 ASN cc_start: 0.9480 (m-40) cc_final: 0.9249 (m-40) REVERT: K 3 VAL cc_start: 0.9345 (t) cc_final: 0.9138 (p) REVERT: K 49 TYR cc_start: 0.9443 (p90) cc_final: 0.9142 (p90) REVERT: K 93 ASN cc_start: 0.9098 (t0) cc_final: 0.8859 (t0) REVERT: K 103 LYS cc_start: 0.9205 (tptm) cc_final: 0.8970 (tptp) outliers start: 35 outliers final: 20 residues processed: 173 average time/residue: 0.1474 time to fit residues: 39.4645 Evaluate side-chains 171 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 8.9990 chunk 131 optimal weight: 0.0980 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.053926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042356 restraints weight = 105458.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044012 restraints weight = 53173.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.045132 restraints weight = 34796.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045874 restraints weight = 26326.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046343 restraints weight = 21842.737| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20334 Z= 0.164 Angle : 0.713 11.361 27798 Z= 0.342 Chirality : 0.045 0.319 3354 Planarity : 0.004 0.050 3366 Dihedral : 5.541 39.361 4326 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.21 % Favored : 93.02 % Rotamer: Outliers : 1.43 % Allowed : 11.81 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.53 (0.17), residues: 2334 helix: 0.55 (0.25), residues: 462 sheet: 0.57 (0.21), residues: 654 loop : -1.26 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 65 TYR 0.049 0.002 TYR E 643 PHE 0.014 0.001 PHE H 78 TRP 0.073 0.002 TRP F 571 HIS 0.005 0.001 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00368 (20205) covalent geometry : angle 0.68833 (27453) SS BOND : bond 0.00316 ( 42) SS BOND : angle 0.70062 ( 84) hydrogen bonds : bond 0.03906 ( 750) hydrogen bonds : angle 5.07160 ( 1953) link_ALPHA1-2 : bond 0.00152 ( 3) link_ALPHA1-2 : angle 1.64072 ( 9) link_ALPHA1-3 : bond 0.00715 ( 3) link_ALPHA1-3 : angle 1.12936 ( 9) link_ALPHA1-6 : bond 0.00381 ( 3) link_ALPHA1-6 : angle 1.48549 ( 9) link_BETA1-4 : bond 0.00273 ( 33) link_BETA1-4 : angle 1.97129 ( 99) link_NAG-ASN : bond 0.00483 ( 45) link_NAG-ASN : angle 2.19326 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: B 566 LEU cc_start: 0.9181 (mt) cc_final: 0.8810 (pp) REVERT: B 574 LYS cc_start: 0.9459 (mtmm) cc_final: 0.8875 (mtmm) REVERT: B 584 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 626 MET cc_start: 0.8362 (mtp) cc_final: 0.7903 (ttt) REVERT: B 639 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 643 TYR cc_start: 0.8939 (m-80) cc_final: 0.8549 (m-80) REVERT: B 656 ASN cc_start: 0.9380 (m-40) cc_final: 0.9085 (m-40) REVERT: H 65 ARG cc_start: 0.8835 (mmm160) cc_final: 0.8631 (mmm160) REVERT: L 3 VAL cc_start: 0.9384 (t) cc_final: 0.9137 (p) REVERT: L 93 ASN cc_start: 0.9075 (t0) cc_final: 0.8832 (t0) REVERT: C 53 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: C 104 MET cc_start: 0.9372 (ttm) cc_final: 0.8976 (ttm) REVERT: C 426 MET cc_start: 0.8668 (ttm) cc_final: 0.8323 (ttm) REVERT: E 530 MET cc_start: 0.8632 (mmm) cc_final: 0.8221 (mmm) REVERT: E 566 LEU cc_start: 0.9215 (mt) cc_final: 0.8814 (pp) REVERT: E 574 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8935 (mtmm) REVERT: E 584 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8526 (tm-30) REVERT: E 626 MET cc_start: 0.8631 (mtp) cc_final: 0.7940 (ttt) REVERT: E 656 ASN cc_start: 0.9454 (m-40) cc_final: 0.9203 (m-40) REVERT: J 103 LYS cc_start: 0.9057 (tptm) cc_final: 0.8811 (tptp) REVERT: D 104 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8830 (ttm) REVERT: D 465 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8093 (m) REVERT: F 566 LEU cc_start: 0.9092 (mt) cc_final: 0.8740 (pp) REVERT: F 584 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8536 (tm-30) REVERT: F 656 ASN cc_start: 0.9473 (m-40) cc_final: 0.9238 (m-40) REVERT: K 3 VAL cc_start: 0.9345 (t) cc_final: 0.9136 (p) REVERT: K 49 TYR cc_start: 0.9441 (p90) cc_final: 0.9155 (p90) REVERT: K 103 LYS cc_start: 0.9202 (tptm) cc_final: 0.8961 (tptp) outliers start: 30 outliers final: 21 residues processed: 179 average time/residue: 0.1379 time to fit residues: 38.4736 Evaluate side-chains 178 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 51 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041231 restraints weight = 110346.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042813 restraints weight = 56414.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043885 restraints weight = 37393.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044589 restraints weight = 28623.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045031 restraints weight = 23978.258| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20334 Z= 0.263 Angle : 0.787 12.250 27798 Z= 0.380 Chirality : 0.046 0.320 3354 Planarity : 0.005 0.076 3366 Dihedral : 5.819 43.215 4326 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.11 % Favored : 92.16 % Rotamer: Outliers : 1.53 % Allowed : 12.53 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -0.65 (0.17), residues: 2334 helix: 0.46 (0.25), residues: 462 sheet: 0.48 (0.21), residues: 654 loop : -1.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 65 TYR 0.034 0.002 TYR E 643 PHE 0.012 0.002 PHE H 78 TRP 0.089 0.002 TRP F 571 HIS 0.007 0.002 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00583 (20205) covalent geometry : angle 0.75995 (27453) SS BOND : bond 0.00486 ( 42) SS BOND : angle 0.84161 ( 84) hydrogen bonds : bond 0.04233 ( 750) hydrogen bonds : angle 5.26961 ( 1953) link_ALPHA1-2 : bond 0.00084 ( 3) link_ALPHA1-2 : angle 1.67707 ( 9) link_ALPHA1-3 : bond 0.00494 ( 3) link_ALPHA1-3 : angle 1.26728 ( 9) link_ALPHA1-6 : bond 0.00364 ( 3) link_ALPHA1-6 : angle 1.48055 ( 9) link_BETA1-4 : bond 0.00270 ( 33) link_BETA1-4 : angle 2.05286 ( 99) link_NAG-ASN : bond 0.00691 ( 45) link_NAG-ASN : angle 2.45044 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.37 seconds wall clock time: 48 minutes 24.31 seconds (2904.31 seconds total)