Starting phenix.real_space_refine on Sun Aug 24 04:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.map" model { file = "/net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flw_29288/08_2025/8flw_29288.cif" } resolution = 3.58 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= 0.004 sd= 0.052 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 119 5.16 5 C 10497 2.51 5 N 2809 2.21 5 O 3443 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16868 Number of models: 1 Model: "" Number of chains: 37 Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "A" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3535 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 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: "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: 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: "O" 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: "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: 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "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: 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: 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: 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 16868 At special positions: 0 Unit cell: (132.126, 128.877, 175.446, 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 119 16.00 O 3443 8.00 N 2809 7.00 C 10497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 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 A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " 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=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.07 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " 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 E 4 " - " MAN E 5 " " MAN N 4 " - " MAN N 5 " " MAN Q 4 " - " MAN Q 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " BMA N 3 " - " MAN N 6 " " BMA Q 3 " - " MAN Q 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 R 2 " - " BMA R 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 301 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 1 " - " ASN C 197 " " NAG E 1 " - " ASN C 262 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 332 " " NAG G 607 " - " ASN G 339 " " NAG G 608 " - " ASN G 355 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 234 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 332 " " NAG I 606 " - " ASN I 339 " " NAG I 607 " - " ASN I 355 " " NAG I 608 " - " ASN I 392 " " NAG I 609 " - " ASN I 137 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 363 " " NAG M 1 " - " ASN C 386 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 276 " " NAG P 1 " - " ASN G 197 " " NAG Q 1 " - " ASN G 262 " " NAG R 1 " - " ASN G 276 " " NAG S 1 " - " ASN G 295 " " NAG T 1 " - " ASN G 363 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN I 197 " " NAG X 1 " - " ASN I 262 " " NAG Y 1 " - " ASN I 276 " " NAG Z 1 " - " ASN I 295 " " NAG a 1 " - " ASN I 363 " " NAG b 1 " - " ASN I 386 " " NAG c 1 " - " ASN I 448 " " NAG d 1 " - " ASN I 160 " " NAG e 1 " - " ASN I 156 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 685.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 23.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'H' and resid 27 through 32 removed outlier: 3.573A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 Processing helix chain 'H' and resid 73 through 76 removed outlier: 4.009A pdb=" N SER H 76 " --> pdb=" O SER H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 73 through 76' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.914A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 4.307A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 3.674A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.690A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 664 removed outlier: 3.516A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.064A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.645A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.645A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 638 No H-bonds generated for 'chain 'B' and resid 636 through 638' Processing helix chain 'B' and resid 639 through 663 removed outlier: 3.717A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.104A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.381A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.547A pdb=" N TRP C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.575A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.656A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.240A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.607A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.819A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.644A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.538A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.076A pdb=" N GLU G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 64' Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.186A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 354 removed outlier: 4.008A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 353 " --> pdb=" O LEU G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 390 removed outlier: 3.640A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 390' Processing helix chain 'G' and resid 476 through 484 removed outlier: 3.522A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.322A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.774A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.799A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR I 341 " --> pdb=" O THR I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 476 through 484 removed outlier: 4.351A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.052A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.963A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA H 88 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 39 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.963A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA H 88 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 39 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS H 35 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU H 93 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR H 94 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU H 105 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 96 " --> pdb=" O ALA H 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.687A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.939A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 75 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.934A pdb=" N HIS L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS L 49 " --> pdb=" O HIS L 53 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR L 36 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL L 104 " --> pdb=" O GLY L 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 603 through 609 removed outlier: 4.697A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 603 through 609 removed outlier: 4.644A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.992A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.886A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.476A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB5, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.654A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 374 through 377 removed outlier: 3.641A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.780A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 603 through 609 removed outlier: 7.384A pdb=" N THR F 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL I 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL F 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.205A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 55 through 56 Processing sheet with id=AC2, first strand: chain 'G' and resid 91 through 94 removed outlier: 4.225A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE G 93 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.573A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.643A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 302 through 309 removed outlier: 6.921A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.594A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD1, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.012A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD3, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.739A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 271 through 273 removed outlier: 4.303A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER I 393 " --> pdb=" O PHE I 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.696A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 305 through 309 removed outlier: 3.696A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2655 1.29 - 1.43: 4464 1.43 - 1.56: 9910 1.56 - 1.70: 2 1.70 - 1.83: 157 Bond restraints: 17188 Sorted by residual: bond pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 1.234 1.160 0.074 1.28e-02 6.10e+03 3.30e+01 bond pdb=" C PRO C 124 " pdb=" O PRO C 124 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.20e-02 6.94e+03 2.88e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.457 0.079 1.71e-02 3.42e+03 2.12e+01 bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.590 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" N PRO C 124 " pdb=" CA PRO C 124 " ideal model delta sigma weight residual 1.468 1.423 0.045 1.10e-02 8.26e+03 1.67e+01 ... (remaining 17183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 22671 2.37 - 4.75: 560 4.75 - 7.12: 95 7.12 - 9.50: 5 9.50 - 11.87: 2 Bond angle restraints: 23333 Sorted by residual: angle pdb=" C THR C 320 " pdb=" CA THR C 320 " pdb=" CB THR C 320 " ideal model delta sigma weight residual 110.19 98.32 11.87 1.64e+00 3.72e-01 5.24e+01 angle pdb=" CA MET I 161 " pdb=" C MET I 161 " pdb=" O MET I 161 " ideal model delta sigma weight residual 121.58 113.61 7.97 1.16e+00 7.43e-01 4.72e+01 angle pdb=" C ASN C 262 " pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " ideal model delta sigma weight residual 111.89 120.76 -8.87 1.42e+00 4.96e-01 3.90e+01 angle pdb=" CA ASN C 262 " pdb=" CB ASN C 262 " pdb=" CG ASN C 262 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" C TYS H 100F" pdb=" CA TYS H 100F" pdb=" CB TYS H 100F" ideal model delta sigma weight residual 110.10 99.40 10.70 1.90e+00 2.77e-01 3.17e+01 ... (remaining 23328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 10636 21.96 - 43.92: 725 43.92 - 65.89: 174 65.89 - 87.85: 75 87.85 - 109.81: 40 Dihedral angle restraints: 11650 sinusoidal: 5972 harmonic: 5678 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 165.49 -72.49 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -147.39 61.39 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -146.06 60.06 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 11647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2884 0.156 - 0.312: 36 0.312 - 0.467: 2 0.467 - 0.623: 0 0.623 - 0.779: 1 Chirality restraints: 2923 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" C1 MAN E 5 " pdb=" O2 MAN E 4 " pdb=" C2 MAN E 5 " pdb=" O5 MAN E 5 " both_signs ideal model delta sigma weight residual False 2.40 2.60 -0.20 2.00e-02 2.50e+03 1.02e+02 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.68e+01 ... (remaining 2920 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.257 2.00e-02 2.50e+03 2.20e-01 6.03e+02 pdb=" C7 NAG E 1 " -0.050 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.368 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " -0.103 2.00e-02 2.50e+03 8.54e-02 9.12e+01 pdb=" C7 NAG O 2 " 0.025 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " -0.076 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " 0.139 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 427 " 0.023 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C TRP C 427 " -0.082 2.00e-02 2.50e+03 pdb=" O TRP C 427 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN C 428 " 0.028 2.00e-02 2.50e+03 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 17 2.29 - 2.95: 8043 2.95 - 3.60: 21806 3.60 - 4.25: 35738 4.25 - 4.90: 60534 Nonbonded interactions: 126138 Sorted by model distance: nonbonded pdb=" OG SER C 447 " pdb=" C1 NAG E 1 " model vdw 1.644 3.470 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.084 3.040 nonbonded pdb=" O THR C 123 " pdb=" OG1 THR C 123 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR A 627 " pdb=" OE1 GLN A 630 " model vdw 2.174 3.040 nonbonded pdb=" O SER C 460 " pdb=" OG1 THR C 461 " model vdw 2.181 3.040 ... (remaining 126133 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 33 through 609) selection = (chain 'G' and resid 33 through 609) selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'c' selection = chain 'd' } 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: 3.070 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.400 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.005 0.089 17327 Z= 0.293 Angle : 0.859 25.802 23713 Z= 0.431 Chirality : 0.056 0.779 2923 Planarity : 0.006 0.220 2834 Dihedral : 17.201 109.809 7867 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.45 % Favored : 95.29 % Rotamer: Outliers : 0.81 % Allowed : 0.64 % Favored : 98.56 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1931 helix: 1.40 (0.31), residues: 336 sheet: -0.01 (0.23), residues: 557 loop : -0.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 166 TYR 0.010 0.001 TYR H 100M PHE 0.011 0.001 PHE I 53 TRP 0.022 0.001 TRP C 427 HIS 0.004 0.000 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00521 (17188) covalent geometry : angle 0.80133 (23333) SS BOND : bond 0.01096 ( 37) SS BOND : angle 1.75997 ( 74) hydrogen bonds : bond 0.27390 ( 493) hydrogen bonds : angle 8.29132 ( 1329) link_ALPHA1-2 : bond 0.00312 ( 4) link_ALPHA1-2 : angle 3.71685 ( 12) link_ALPHA1-3 : bond 0.00447 ( 4) link_ALPHA1-3 : angle 2.05453 ( 12) link_ALPHA1-6 : bond 0.00924 ( 4) link_ALPHA1-6 : angle 3.09126 ( 12) link_BETA1-4 : bond 0.00379 ( 32) link_BETA1-4 : angle 2.06021 ( 96) link_NAG-ASN : bond 0.01268 ( 58) link_NAG-ASN : angle 2.98049 ( 174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 371 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 51 MET cc_start: 0.6359 (ppp) cc_final: 0.6075 (ppp) REVERT: L 32 TYR cc_start: 0.7241 (m-80) cc_final: 0.6620 (m-80) REVERT: A 579 ARG cc_start: 0.8921 (mtp180) cc_final: 0.8610 (mtm180) REVERT: A 586 TYR cc_start: 0.8989 (t80) cc_final: 0.8741 (t80) REVERT: A 601 LYS cc_start: 0.8357 (mtpt) cc_final: 0.7944 (mttp) REVERT: B 638 TYR cc_start: 0.5916 (m-80) cc_final: 0.5709 (m-80) REVERT: C 153 GLU cc_start: 0.6960 (tp30) cc_final: 0.6613 (tp30) REVERT: F 591 GLN cc_start: 0.7896 (tt0) cc_final: 0.7654 (tt0) REVERT: G 111 LEU cc_start: 0.8966 (mt) cc_final: 0.8734 (mt) REVERT: G 112 TRP cc_start: 0.8009 (t-100) cc_final: 0.7683 (t-100) REVERT: I 35 TRP cc_start: 0.7819 (m100) cc_final: 0.7540 (m100) REVERT: I 38 VAL cc_start: 0.9091 (p) cc_final: 0.8805 (m) REVERT: I 104 MET cc_start: 0.8408 (ttt) cc_final: 0.8202 (ttt) REVERT: I 217 TYR cc_start: 0.8252 (m-80) cc_final: 0.8038 (m-80) REVERT: I 475 MET cc_start: 0.8495 (tpp) cc_final: 0.8084 (tpp) outliers start: 14 outliers final: 6 residues processed: 381 average time/residue: 0.1191 time to fit residues: 67.8372 Evaluate side-chains 217 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain G residue 121 LYS Chi-restraints excluded: chain G residue 205 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 93 HIS A 543 ASN B 543 ASN B 625 ASN C 103 GLN C 105 HIS C 185 ASN C 195 ASN C 203 GLN F 630 GLN G 99 ASN G 203 GLN G 246 GLN G 280 ASN I 114 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.173872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141151 restraints weight = 23461.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143805 restraints weight = 17317.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145377 restraints weight = 14204.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146244 restraints weight = 12210.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.146292 restraints weight = 11146.986| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17327 Z= 0.159 Angle : 0.750 24.824 23713 Z= 0.343 Chirality : 0.049 0.382 2923 Planarity : 0.004 0.033 2834 Dihedral : 13.068 82.214 4212 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.37 % Allowed : 9.87 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.19), residues: 1931 helix: 1.32 (0.28), residues: 339 sheet: 0.26 (0.23), residues: 519 loop : -0.39 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 350 TYR 0.024 0.002 TYR H 91 PHE 0.025 0.002 PHE C 53 TRP 0.017 0.001 TRP A 631 HIS 0.005 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00351 (17188) covalent geometry : angle 0.68111 (23333) SS BOND : bond 0.00436 ( 37) SS BOND : angle 1.41644 ( 74) hydrogen bonds : bond 0.06203 ( 493) hydrogen bonds : angle 5.82846 ( 1329) link_ALPHA1-2 : bond 0.00441 ( 4) link_ALPHA1-2 : angle 2.02625 ( 12) link_ALPHA1-3 : bond 0.01244 ( 4) link_ALPHA1-3 : angle 1.93934 ( 12) link_ALPHA1-6 : bond 0.00499 ( 4) link_ALPHA1-6 : angle 2.02462 ( 12) link_BETA1-4 : bond 0.00522 ( 32) link_BETA1-4 : angle 1.87592 ( 96) link_NAG-ASN : bond 0.00476 ( 58) link_NAG-ASN : angle 3.30370 ( 174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.5130 (mpp) cc_final: 0.4802 (mpp) REVERT: H 100 PHE cc_start: 0.8438 (p90) cc_final: 0.7999 (p90) REVERT: A 542 ARG cc_start: 0.8307 (ttp-170) cc_final: 0.8105 (ttp-170) REVERT: A 601 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7866 (mttp) REVERT: C 153 GLU cc_start: 0.7398 (tp30) cc_final: 0.7005 (tp30) REVERT: C 198 THR cc_start: 0.9244 (m) cc_final: 0.8949 (p) REVERT: C 475 MET cc_start: 0.8202 (tpp) cc_final: 0.8001 (tpt) REVERT: F 571 TRP cc_start: 0.8150 (m100) cc_final: 0.7852 (m100) REVERT: G 112 TRP cc_start: 0.8151 (t-100) cc_final: 0.7737 (t-100) REVERT: G 456 ARG cc_start: 0.8145 (ptm-80) cc_final: 0.7916 (tmm-80) REVERT: I 38 VAL cc_start: 0.9093 (p) cc_final: 0.8871 (m) REVERT: I 428 GLN cc_start: 0.8098 (mp10) cc_final: 0.7819 (mt0) REVERT: I 475 MET cc_start: 0.8303 (tpp) cc_final: 0.7972 (tpp) outliers start: 41 outliers final: 26 residues processed: 270 average time/residue: 0.1085 time to fit residues: 45.1534 Evaluate side-chains 232 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 340 GLU Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 90 GLN L 93 HIS F 591 GLN F 640 GLN G 99 ASN G 203 GLN G 249 HIS I 374 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.167423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134502 restraints weight = 23964.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135915 restraints weight = 17836.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138579 restraints weight = 14649.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139266 restraints weight = 11868.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139392 restraints weight = 10903.989| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17327 Z= 0.206 Angle : 0.742 15.919 23713 Z= 0.338 Chirality : 0.051 0.853 2923 Planarity : 0.004 0.045 2834 Dihedral : 11.366 73.635 4201 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.41 % Allowed : 12.36 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.19), residues: 1931 helix: 0.62 (0.28), residues: 378 sheet: 0.05 (0.23), residues: 545 loop : -0.44 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 585 TYR 0.020 0.002 TYR A 586 PHE 0.021 0.002 PHE C 53 TRP 0.014 0.001 TRP A 631 HIS 0.005 0.001 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00488 (17188) covalent geometry : angle 0.68385 (23333) SS BOND : bond 0.00430 ( 37) SS BOND : angle 1.15147 ( 74) hydrogen bonds : bond 0.05463 ( 493) hydrogen bonds : angle 5.39412 ( 1329) link_ALPHA1-2 : bond 0.00385 ( 4) link_ALPHA1-2 : angle 1.92579 ( 12) link_ALPHA1-3 : bond 0.01119 ( 4) link_ALPHA1-3 : angle 1.85111 ( 12) link_ALPHA1-6 : bond 0.00333 ( 4) link_ALPHA1-6 : angle 1.90069 ( 12) link_BETA1-4 : bond 0.00497 ( 32) link_BETA1-4 : angle 1.72156 ( 96) link_NAG-ASN : bond 0.00429 ( 58) link_NAG-ASN : angle 3.04799 ( 174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 39 GLN cc_start: 0.5029 (tt0) cc_final: 0.4758 (tt0) REVERT: H 80 MET cc_start: 0.5198 (mpp) cc_final: 0.4964 (mpp) REVERT: H 100 PHE cc_start: 0.8588 (p90) cc_final: 0.8247 (p90) REVERT: L 31 ASN cc_start: 0.8469 (p0) cc_final: 0.8107 (p0) REVERT: A 542 ARG cc_start: 0.8467 (ttp-170) cc_final: 0.8188 (ttp-170) REVERT: A 601 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8162 (mtmm) REVERT: C 153 GLU cc_start: 0.7494 (tp30) cc_final: 0.7013 (tp30) REVERT: G 112 TRP cc_start: 0.8197 (t-100) cc_final: 0.7981 (t60) REVERT: G 475 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7437 (ptm) REVERT: I 38 VAL cc_start: 0.9249 (p) cc_final: 0.8991 (m) REVERT: I 271 MET cc_start: 0.7586 (mtt) cc_final: 0.7351 (mtt) REVERT: I 475 MET cc_start: 0.8342 (tpp) cc_final: 0.8037 (tpp) outliers start: 59 outliers final: 40 residues processed: 253 average time/residue: 0.1053 time to fit residues: 41.4619 Evaluate side-chains 241 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 HIS C 136 ASN F 640 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135463 restraints weight = 23620.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137210 restraints weight = 16815.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139022 restraints weight = 14085.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139813 restraints weight = 12204.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140132 restraints weight = 11282.779| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17327 Z= 0.150 Angle : 0.674 12.798 23713 Z= 0.308 Chirality : 0.047 0.394 2923 Planarity : 0.003 0.028 2834 Dihedral : 10.121 70.026 4201 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.06 % Allowed : 14.38 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.19), residues: 1931 helix: 0.69 (0.28), residues: 378 sheet: 0.20 (0.23), residues: 511 loop : -0.50 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.017 0.001 TYR H 91 PHE 0.018 0.001 PHE C 53 TRP 0.015 0.001 TRP H 108 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00350 (17188) covalent geometry : angle 0.62578 (23333) SS BOND : bond 0.00305 ( 37) SS BOND : angle 0.96222 ( 74) hydrogen bonds : bond 0.04480 ( 493) hydrogen bonds : angle 5.00669 ( 1329) link_ALPHA1-2 : bond 0.00350 ( 4) link_ALPHA1-2 : angle 1.82511 ( 12) link_ALPHA1-3 : bond 0.01214 ( 4) link_ALPHA1-3 : angle 1.97223 ( 12) link_ALPHA1-6 : bond 0.00521 ( 4) link_ALPHA1-6 : angle 1.80774 ( 12) link_BETA1-4 : bond 0.00454 ( 32) link_BETA1-4 : angle 1.62600 ( 96) link_NAG-ASN : bond 0.00434 ( 58) link_NAG-ASN : angle 2.62389 ( 174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 0.454 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: H 39 GLN cc_start: 0.5134 (tt0) cc_final: 0.4921 (tt0) REVERT: H 100 PHE cc_start: 0.8583 (p90) cc_final: 0.8217 (p90) REVERT: L 31 ASN cc_start: 0.8363 (p0) cc_final: 0.8140 (p0) REVERT: A 586 TYR cc_start: 0.9015 (t80) cc_final: 0.8812 (t80) REVERT: A 601 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8167 (mtmm) REVERT: A 615 SER cc_start: 0.8378 (t) cc_final: 0.8090 (m) REVERT: G 111 LEU cc_start: 0.8829 (mt) cc_final: 0.8605 (mt) REVERT: G 217 TYR cc_start: 0.8019 (m-80) cc_final: 0.7051 (m-80) REVERT: G 475 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7259 (ptm) REVERT: I 38 VAL cc_start: 0.9140 (p) cc_final: 0.8881 (m) REVERT: I 104 MET cc_start: 0.8562 (ttt) cc_final: 0.8302 (ttt) outliers start: 53 outliers final: 33 residues processed: 251 average time/residue: 0.1049 time to fit residues: 41.7196 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 160 optimal weight: 0.0040 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN F 630 GLN F 640 GLN G 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135998 restraints weight = 23742.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137462 restraints weight = 17499.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138870 restraints weight = 14521.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140071 restraints weight = 12902.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140782 restraints weight = 11492.115| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17327 Z= 0.127 Angle : 0.665 14.648 23713 Z= 0.303 Chirality : 0.046 0.381 2923 Planarity : 0.003 0.057 2834 Dihedral : 9.242 67.137 4201 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.71 % Allowed : 15.59 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.19), residues: 1931 helix: 0.81 (0.28), residues: 378 sheet: 0.07 (0.22), residues: 547 loop : -0.51 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.013 0.001 TYR I 173 PHE 0.016 0.001 PHE C 53 TRP 0.010 0.001 TRP G 338 HIS 0.005 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00293 (17188) covalent geometry : angle 0.61450 (23333) SS BOND : bond 0.00264 ( 37) SS BOND : angle 2.01574 ( 74) hydrogen bonds : bond 0.04062 ( 493) hydrogen bonds : angle 4.79906 ( 1329) link_ALPHA1-2 : bond 0.00362 ( 4) link_ALPHA1-2 : angle 1.73830 ( 12) link_ALPHA1-3 : bond 0.01217 ( 4) link_ALPHA1-3 : angle 1.84333 ( 12) link_ALPHA1-6 : bond 0.00721 ( 4) link_ALPHA1-6 : angle 1.59120 ( 12) link_BETA1-4 : bond 0.00453 ( 32) link_BETA1-4 : angle 1.49964 ( 96) link_NAG-ASN : bond 0.00381 ( 58) link_NAG-ASN : angle 2.46710 ( 174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8590 (p90) cc_final: 0.8213 (p90) REVERT: L 31 ASN cc_start: 0.8389 (p0) cc_final: 0.8072 (p0) REVERT: L 90 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6963 (pp30) REVERT: A 601 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8025 (mttp) REVERT: A 615 SER cc_start: 0.8401 (t) cc_final: 0.8138 (m) REVERT: F 540 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: G 217 TYR cc_start: 0.8019 (m-80) cc_final: 0.7090 (m-80) REVERT: G 475 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7095 (ptm) REVERT: I 38 VAL cc_start: 0.9101 (p) cc_final: 0.8835 (m) REVERT: I 104 MET cc_start: 0.8543 (ttt) cc_final: 0.8284 (ttt) outliers start: 47 outliers final: 29 residues processed: 250 average time/residue: 0.1074 time to fit residues: 41.3644 Evaluate side-chains 240 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 104 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 90 GLN A 652 GLN F 640 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.166801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134961 restraints weight = 23638.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135959 restraints weight = 18643.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138271 restraints weight = 15709.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139020 restraints weight = 12687.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.139105 restraints weight = 11751.767| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17327 Z= 0.153 Angle : 0.683 13.992 23713 Z= 0.310 Chirality : 0.047 0.393 2923 Planarity : 0.003 0.047 2834 Dihedral : 8.831 58.623 4200 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.89 % Allowed : 16.63 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 1931 helix: 0.56 (0.28), residues: 396 sheet: 0.06 (0.22), residues: 543 loop : -0.60 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 39 TYR 0.020 0.001 TYR L 87 PHE 0.016 0.001 PHE C 53 TRP 0.009 0.001 TRP C 112 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00362 (17188) covalent geometry : angle 0.63750 (23333) SS BOND : bond 0.00254 ( 37) SS BOND : angle 1.58604 ( 74) hydrogen bonds : bond 0.04121 ( 493) hydrogen bonds : angle 4.78685 ( 1329) link_ALPHA1-2 : bond 0.00327 ( 4) link_ALPHA1-2 : angle 1.75949 ( 12) link_ALPHA1-3 : bond 0.01214 ( 4) link_ALPHA1-3 : angle 1.85452 ( 12) link_ALPHA1-6 : bond 0.00748 ( 4) link_ALPHA1-6 : angle 1.55781 ( 12) link_BETA1-4 : bond 0.00457 ( 32) link_BETA1-4 : angle 1.47555 ( 96) link_NAG-ASN : bond 0.00376 ( 58) link_NAG-ASN : angle 2.47018 ( 174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8618 (p90) cc_final: 0.8332 (p90) REVERT: L 31 ASN cc_start: 0.8255 (p0) cc_final: 0.7917 (p0) REVERT: L 90 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7039 (pp30) REVERT: A 601 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8016 (mttp) REVERT: A 615 SER cc_start: 0.8471 (t) cc_final: 0.8226 (m) REVERT: F 540 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: G 217 TYR cc_start: 0.8091 (m-80) cc_final: 0.7150 (m-80) REVERT: G 322 ILE cc_start: 0.8781 (mm) cc_final: 0.8559 (mt) REVERT: G 475 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7026 (ptm) REVERT: I 38 VAL cc_start: 0.9140 (p) cc_final: 0.8892 (m) REVERT: I 474 ASP cc_start: 0.6024 (t0) cc_final: 0.5800 (t0) outliers start: 50 outliers final: 37 residues processed: 238 average time/residue: 0.1141 time to fit residues: 42.0954 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 chunk 149 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN F 640 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.167880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130858 restraints weight = 23711.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133724 restraints weight = 19156.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135248 restraints weight = 14837.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136191 restraints weight = 13221.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136260 restraints weight = 12180.079| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17327 Z= 0.158 Angle : 0.678 14.872 23713 Z= 0.310 Chirality : 0.046 0.396 2923 Planarity : 0.003 0.061 2834 Dihedral : 8.543 58.299 4200 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.89 % Allowed : 16.92 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1931 helix: 0.56 (0.28), residues: 396 sheet: 0.07 (0.22), residues: 541 loop : -0.62 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 617 TYR 0.018 0.001 TYR A 586 PHE 0.015 0.001 PHE C 53 TRP 0.009 0.001 TRP G 69 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00375 (17188) covalent geometry : angle 0.63338 (23333) SS BOND : bond 0.00322 ( 37) SS BOND : angle 1.57857 ( 74) hydrogen bonds : bond 0.04095 ( 493) hydrogen bonds : angle 4.75838 ( 1329) link_ALPHA1-2 : bond 0.00312 ( 4) link_ALPHA1-2 : angle 1.75484 ( 12) link_ALPHA1-3 : bond 0.01278 ( 4) link_ALPHA1-3 : angle 1.81882 ( 12) link_ALPHA1-6 : bond 0.00728 ( 4) link_ALPHA1-6 : angle 1.57753 ( 12) link_BETA1-4 : bond 0.00457 ( 32) link_BETA1-4 : angle 1.46897 ( 96) link_NAG-ASN : bond 0.00375 ( 58) link_NAG-ASN : angle 2.43348 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8629 (p90) cc_final: 0.8331 (p90) REVERT: L 31 ASN cc_start: 0.8388 (p0) cc_final: 0.7918 (p0) REVERT: A 601 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8169 (mtmm) REVERT: A 615 SER cc_start: 0.8470 (t) cc_final: 0.8210 (m) REVERT: F 540 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: G 217 TYR cc_start: 0.8206 (m-80) cc_final: 0.7314 (m-80) REVERT: G 322 ILE cc_start: 0.8836 (mm) cc_final: 0.8635 (mt) REVERT: G 475 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7107 (ptm) REVERT: I 38 VAL cc_start: 0.9114 (p) cc_final: 0.8837 (m) outliers start: 50 outliers final: 38 residues processed: 234 average time/residue: 0.1068 time to fit residues: 39.6885 Evaluate side-chains 234 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 134 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 110 HIS L 100 GLN F 640 GLN G 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.167144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129797 restraints weight = 23903.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.133601 restraints weight = 18580.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135185 restraints weight = 14574.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135487 restraints weight = 12692.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.135915 restraints weight = 11946.688| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17327 Z= 0.154 Angle : 0.679 15.133 23713 Z= 0.311 Chirality : 0.046 0.398 2923 Planarity : 0.003 0.047 2834 Dihedral : 8.191 58.142 4200 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.77 % Allowed : 17.67 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.19), residues: 1931 helix: 0.56 (0.28), residues: 396 sheet: 0.05 (0.22), residues: 543 loop : -0.63 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 38 TYR 0.017 0.001 TYR A 586 PHE 0.015 0.001 PHE C 53 TRP 0.010 0.001 TRP G 69 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00366 (17188) covalent geometry : angle 0.63838 (23333) SS BOND : bond 0.00271 ( 37) SS BOND : angle 1.49436 ( 74) hydrogen bonds : bond 0.04023 ( 493) hydrogen bonds : angle 4.70330 ( 1329) link_ALPHA1-2 : bond 0.00343 ( 4) link_ALPHA1-2 : angle 1.73921 ( 12) link_ALPHA1-3 : bond 0.01144 ( 4) link_ALPHA1-3 : angle 1.74300 ( 12) link_ALPHA1-6 : bond 0.00722 ( 4) link_ALPHA1-6 : angle 1.59416 ( 12) link_BETA1-4 : bond 0.00460 ( 32) link_BETA1-4 : angle 1.46009 ( 96) link_NAG-ASN : bond 0.00365 ( 58) link_NAG-ASN : angle 2.35699 ( 174) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8585 (p90) cc_final: 0.8335 (p90) REVERT: L 31 ASN cc_start: 0.8448 (p0) cc_final: 0.7966 (p0) REVERT: A 601 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8046 (mttp) REVERT: F 540 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: G 475 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6981 (ptm) REVERT: I 38 VAL cc_start: 0.9119 (p) cc_final: 0.8855 (m) outliers start: 48 outliers final: 38 residues processed: 235 average time/residue: 0.1106 time to fit residues: 40.5502 Evaluate side-chains 235 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 100 GLN C 99 ASN C 103 GLN F 630 GLN F 640 GLN I 105 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130449 restraints weight = 23758.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133898 restraints weight = 17768.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135007 restraints weight = 14634.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135439 restraints weight = 12904.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135587 restraints weight = 11835.291| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17327 Z= 0.149 Angle : 0.670 16.583 23713 Z= 0.307 Chirality : 0.046 0.397 2923 Planarity : 0.003 0.039 2834 Dihedral : 8.032 58.926 4200 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.66 % Allowed : 17.90 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.19), residues: 1931 helix: 0.57 (0.28), residues: 396 sheet: 0.08 (0.22), residues: 543 loop : -0.64 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.016 0.001 TYR A 586 PHE 0.014 0.001 PHE C 53 TRP 0.023 0.001 TRP C 69 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00356 (17188) covalent geometry : angle 0.62943 (23333) SS BOND : bond 0.00274 ( 37) SS BOND : angle 1.44877 ( 74) hydrogen bonds : bond 0.03913 ( 493) hydrogen bonds : angle 4.67365 ( 1329) link_ALPHA1-2 : bond 0.00347 ( 4) link_ALPHA1-2 : angle 1.72665 ( 12) link_ALPHA1-3 : bond 0.01073 ( 4) link_ALPHA1-3 : angle 1.70320 ( 12) link_ALPHA1-6 : bond 0.00677 ( 4) link_ALPHA1-6 : angle 1.60639 ( 12) link_BETA1-4 : bond 0.00456 ( 32) link_BETA1-4 : angle 1.45680 ( 96) link_NAG-ASN : bond 0.00374 ( 58) link_NAG-ASN : angle 2.31987 ( 174) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8597 (p90) cc_final: 0.8336 (p90) REVERT: L 31 ASN cc_start: 0.8481 (p0) cc_final: 0.8020 (p0) REVERT: L 90 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.6968 (pp30) REVERT: A 542 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.8044 (ttp-170) REVERT: A 601 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8050 (mttp) REVERT: F 540 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: G 217 TYR cc_start: 0.8324 (m-80) cc_final: 0.7529 (m-80) REVERT: G 475 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6993 (ptm) REVERT: I 38 VAL cc_start: 0.9122 (p) cc_final: 0.8859 (m) outliers start: 46 outliers final: 40 residues processed: 234 average time/residue: 0.1186 time to fit residues: 42.9438 Evaluate side-chains 241 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 100 GLN C 99 ASN C 103 GLN F 630 GLN F 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131230 restraints weight = 23779.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135335 restraints weight = 17604.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135992 restraints weight = 14168.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136827 restraints weight = 12717.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137019 restraints weight = 11786.115| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17327 Z= 0.136 Angle : 0.667 17.520 23713 Z= 0.305 Chirality : 0.046 0.392 2923 Planarity : 0.003 0.056 2834 Dihedral : 7.935 58.600 4200 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.60 % Allowed : 18.24 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.19), residues: 1931 helix: 0.61 (0.28), residues: 396 sheet: 0.10 (0.22), residues: 543 loop : -0.63 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.016 0.001 TYR A 586 PHE 0.015 0.001 PHE C 53 TRP 0.024 0.001 TRP C 69 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00319 (17188) covalent geometry : angle 0.62859 (23333) SS BOND : bond 0.00318 ( 37) SS BOND : angle 1.36299 ( 74) hydrogen bonds : bond 0.03810 ( 493) hydrogen bonds : angle 4.64924 ( 1329) link_ALPHA1-2 : bond 0.00333 ( 4) link_ALPHA1-2 : angle 1.70744 ( 12) link_ALPHA1-3 : bond 0.01076 ( 4) link_ALPHA1-3 : angle 1.66148 ( 12) link_ALPHA1-6 : bond 0.00692 ( 4) link_ALPHA1-6 : angle 1.60701 ( 12) link_BETA1-4 : bond 0.00456 ( 32) link_BETA1-4 : angle 1.44757 ( 96) link_NAG-ASN : bond 0.00370 ( 58) link_NAG-ASN : angle 2.26154 ( 174) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3862 Ramachandran restraints generated. 1931 Oldfield, 0 Emsley, 1931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8582 (p90) cc_final: 0.8319 (p90) REVERT: L 31 ASN cc_start: 0.8510 (p0) cc_final: 0.8014 (p0) REVERT: A 601 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8009 (mttp) REVERT: F 540 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: G 217 TYR cc_start: 0.8316 (m-80) cc_final: 0.7515 (m-80) REVERT: G 475 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6920 (ptm) REVERT: I 38 VAL cc_start: 0.9117 (p) cc_final: 0.8856 (m) REVERT: I 370 GLU cc_start: 0.7985 (mp0) cc_final: 0.7752 (mp0) outliers start: 45 outliers final: 38 residues processed: 233 average time/residue: 0.1069 time to fit residues: 38.6116 Evaluate side-chains 238 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 LYS Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain G residue 475 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 364 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 54 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN F 630 GLN G 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127350 restraints weight = 23822.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.132896 restraints weight = 18521.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133969 restraints weight = 13500.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134018 restraints weight = 11527.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134523 restraints weight = 11534.640| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17327 Z= 0.202 Angle : 0.724 17.731 23713 Z= 0.334 Chirality : 0.048 0.414 2923 Planarity : 0.003 0.036 2834 Dihedral : 8.063 59.167 4200 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.54 % Allowed : 18.65 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.19), residues: 1931 helix: 0.39 (0.27), residues: 408 sheet: 0.03 (0.22), residues: 529 loop : -0.75 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 542 TYR 0.018 0.002 TYR A 586 PHE 0.014 0.002 PHE C 53 TRP 0.028 0.002 TRP C 69 HIS 0.006 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00488 (17188) covalent geometry : angle 0.68578 (23333) SS BOND : bond 0.00293 ( 37) SS BOND : angle 1.57448 ( 74) hydrogen bonds : bond 0.04307 ( 493) hydrogen bonds : angle 4.83283 ( 1329) link_ALPHA1-2 : bond 0.00330 ( 4) link_ALPHA1-2 : angle 1.83920 ( 12) link_ALPHA1-3 : bond 0.01021 ( 4) link_ALPHA1-3 : angle 1.89022 ( 12) link_ALPHA1-6 : bond 0.00575 ( 4) link_ALPHA1-6 : angle 1.60016 ( 12) link_BETA1-4 : bond 0.00476 ( 32) link_BETA1-4 : angle 1.47556 ( 96) link_NAG-ASN : bond 0.00404 ( 58) link_NAG-ASN : angle 2.32820 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.56 seconds wall clock time: 40 minutes 7.31 seconds (2407.31 seconds total)