Starting phenix.real_space_refine on Sun Jun 15 08:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flw_29288/06_2025/8flw_29288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flw_29288/06_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_29288/06_2025/8flw_29288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flw_29288/06_2025/8flw_29288.map" model { file = "/net/cci-nas-00/data/ceres_data/8flw_29288/06_2025/8flw_29288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flw_29288/06_2025/8flw_29288.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.43, per 1000 atoms: 0.68 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: 5.55 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.44 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: 6.42 Time building geometry restraints manager: 6.42 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 505 or resid 601 through 609)) selection = (chain 'G' and (resid 33 through 505 or resid 601 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.350 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 52.900 ------------------------------------------------------------------------------- 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 : 4.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.001 TRP C 427 HIS 0.004 0.000 HIS C 249 PHE 0.011 0.001 PHE I 53 TYR 0.010 0.001 TYR H 100M ARG 0.008 0.000 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.01268 ( 58) link_NAG-ASN : angle 2.98049 ( 174) 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_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) hydrogen bonds : bond 0.27390 ( 493) hydrogen bonds : angle 8.29132 ( 1329) SS BOND : bond 0.01096 ( 37) SS BOND : angle 1.75997 ( 74) covalent geometry : bond 0.00521 (17188) covalent geometry : angle 0.80133 (23333) *********************** 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 : 1.733 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: 0.3052 time to fit residues: 172.2572 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 : 1.955 ------------------------------------------------------------------------------- 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 165 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 177 optimal weight: 3.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- 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 105 HIS C 185 ASN C 203 GLN F 630 GLN G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 280 ASN I 114 GLN I 374 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.171784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139273 restraints weight = 23614.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140462 restraints weight = 18547.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143477 restraints weight = 15337.007| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2172 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= 0.189 Angle : 0.771 25.292 23713 Z= 0.354 Chirality : 0.049 0.398 2923 Planarity : 0.004 0.034 2834 Dihedral : 13.157 82.108 4212 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.66 % Allowed : 9.47 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1931 helix: 1.27 (0.28), residues: 339 sheet: 0.11 (0.23), residues: 556 loop : -0.39 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 631 HIS 0.005 0.001 HIS G 105 PHE 0.023 0.002 PHE C 53 TYR 0.023 0.002 TYR H 91 ARG 0.005 0.001 ARG C 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 58) link_NAG-ASN : angle 3.39175 ( 174) link_ALPHA1-6 : bond 0.00440 ( 4) link_ALPHA1-6 : angle 1.96429 ( 12) link_BETA1-4 : bond 0.00492 ( 32) link_BETA1-4 : angle 1.82840 ( 96) link_ALPHA1-2 : bond 0.00467 ( 4) link_ALPHA1-2 : angle 2.14395 ( 12) link_ALPHA1-3 : bond 0.01178 ( 4) link_ALPHA1-3 : angle 1.91951 ( 12) hydrogen bonds : bond 0.06367 ( 493) hydrogen bonds : angle 5.88573 ( 1329) SS BOND : bond 0.00369 ( 37) SS BOND : angle 1.42415 ( 74) covalent geometry : bond 0.00437 (17188) covalent geometry : angle 0.70161 (23333) *********************** 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 279 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 80 MET cc_start: 0.5142 (mpp) cc_final: 0.4821 (mpp) REVERT: H 100 PHE cc_start: 0.8456 (p90) cc_final: 0.7996 (p90) REVERT: A 601 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7966 (mttp) REVERT: B 592 LEU cc_start: 0.8979 (tp) cc_final: 0.8752 (tp) REVERT: C 153 GLU cc_start: 0.7434 (tp30) cc_final: 0.7001 (tp30) REVERT: C 198 THR cc_start: 0.9275 (m) cc_final: 0.8931 (p) REVERT: F 571 TRP cc_start: 0.8111 (m100) cc_final: 0.7765 (m100) REVERT: G 111 LEU cc_start: 0.8917 (mt) cc_final: 0.8694 (mt) REVERT: G 112 TRP cc_start: 0.8201 (t-100) cc_final: 0.7994 (t-100) REVERT: G 456 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7961 (tmm-80) REVERT: I 38 VAL cc_start: 0.9120 (p) cc_final: 0.8866 (m) REVERT: I 104 MET cc_start: 0.8349 (ttt) cc_final: 0.8131 (ttt) REVERT: I 349 LEU cc_start: 0.8201 (mt) cc_final: 0.7989 (mp) REVERT: I 475 MET cc_start: 0.8276 (tpp) cc_final: 0.7966 (tpp) outliers start: 46 outliers final: 33 residues processed: 262 average time/residue: 0.2686 time to fit residues: 108.2988 Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 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 B residue 599 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 642 ILE 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 F residue 528 SER 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 257 THR 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 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133586 restraints weight = 23593.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138307 restraints weight = 18125.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140680 restraints weight = 13089.295| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2797 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= 0.179 Angle : 0.720 16.882 23713 Z= 0.326 Chirality : 0.050 0.825 2923 Planarity : 0.004 0.042 2834 Dihedral : 11.284 74.364 4201 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.18 % Allowed : 12.64 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 1931 helix: 0.66 (0.28), residues: 378 sheet: 0.06 (0.23), residues: 545 loop : -0.44 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 631 HIS 0.005 0.001 HIS G 352 PHE 0.022 0.002 PHE C 53 TYR 0.020 0.002 TYR A 586 ARG 0.004 0.000 ARG A 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 58) link_NAG-ASN : angle 2.77787 ( 174) link_ALPHA1-6 : bond 0.00383 ( 4) link_ALPHA1-6 : angle 1.88763 ( 12) link_BETA1-4 : bond 0.00522 ( 32) link_BETA1-4 : angle 1.71620 ( 96) link_ALPHA1-2 : bond 0.00415 ( 4) link_ALPHA1-2 : angle 1.88874 ( 12) link_ALPHA1-3 : bond 0.01345 ( 4) link_ALPHA1-3 : angle 1.94318 ( 12) hydrogen bonds : bond 0.05208 ( 493) hydrogen bonds : angle 5.31590 ( 1329) SS BOND : bond 0.00319 ( 37) SS BOND : angle 1.10146 ( 74) covalent geometry : bond 0.00420 (17188) covalent geometry : angle 0.66918 (23333) *********************** 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 269 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 1.705 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: 0.5336 (mpp) cc_final: 0.5127 (mpp) REVERT: H 100 PHE cc_start: 0.8563 (p90) cc_final: 0.8220 (p90) REVERT: A 601 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8135 (mtmm) REVERT: F 626 MET cc_start: 0.8047 (ttm) cc_final: 0.7822 (ttm) REVERT: G 112 TRP cc_start: 0.8356 (t-100) cc_final: 0.7966 (t-100) REVERT: G 114 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7926 (tm-30) REVERT: G 475 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7352 (ptm) REVERT: I 38 VAL cc_start: 0.9235 (p) cc_final: 0.8975 (m) REVERT: I 475 MET cc_start: 0.8297 (tpp) cc_final: 0.8031 (tpp) outliers start: 55 outliers final: 32 residues processed: 246 average time/residue: 0.2779 time to fit residues: 104.1997 Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 THR 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 642 ILE 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 488 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 152 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0050 chunk 157 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN G 85 HIS ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135496 restraints weight = 23581.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136838 restraints weight = 17908.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.139534 restraints weight = 14702.941| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17327 Z= 0.143 Angle : 0.674 12.512 23713 Z= 0.308 Chirality : 0.047 0.395 2923 Planarity : 0.003 0.029 2834 Dihedral : 9.945 63.642 4201 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.89 % Allowed : 14.15 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1931 helix: 0.76 (0.28), residues: 378 sheet: 0.00 (0.23), residues: 541 loop : -0.53 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 45 HIS 0.004 0.001 HIS C 249 PHE 0.018 0.001 PHE C 53 TYR 0.015 0.002 TYR I 173 ARG 0.007 0.000 ARG A 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 58) link_NAG-ASN : angle 2.61804 ( 174) link_ALPHA1-6 : bond 0.00541 ( 4) link_ALPHA1-6 : angle 1.75242 ( 12) link_BETA1-4 : bond 0.00442 ( 32) link_BETA1-4 : angle 1.60369 ( 96) link_ALPHA1-2 : bond 0.00359 ( 4) link_ALPHA1-2 : angle 1.83150 ( 12) link_ALPHA1-3 : bond 0.01138 ( 4) link_ALPHA1-3 : angle 1.94554 ( 12) hydrogen bonds : bond 0.04346 ( 493) hydrogen bonds : angle 4.94768 ( 1329) SS BOND : bond 0.00337 ( 37) SS BOND : angle 1.67309 ( 74) covalent geometry : bond 0.00334 (17188) covalent geometry : angle 0.62152 (23333) *********************** 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 267 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8581 (p90) cc_final: 0.8225 (p90) REVERT: L 31 ASN cc_start: 0.8390 (p0) cc_final: 0.8076 (p0) REVERT: A 586 TYR cc_start: 0.9017 (t80) cc_final: 0.8816 (t80) REVERT: A 601 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8170 (mtmm) REVERT: A 615 SER cc_start: 0.8379 (t) cc_final: 0.8100 (m) REVERT: G 111 LEU cc_start: 0.8869 (mt) cc_final: 0.8648 (mt) REVERT: G 112 TRP cc_start: 0.8237 (t-100) cc_final: 0.7976 (t60) REVERT: G 217 TYR cc_start: 0.7996 (m-80) cc_final: 0.7068 (m-80) REVERT: G 475 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7263 (ptm) REVERT: I 38 VAL cc_start: 0.9093 (p) cc_final: 0.8822 (m) REVERT: I 104 MET cc_start: 0.8539 (ttt) cc_final: 0.8279 (ttt) outliers start: 50 outliers final: 28 residues processed: 249 average time/residue: 0.2626 time to fit residues: 100.5194 Evaluate side-chains 228 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE 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 433 CYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 47 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 640 GLN I 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131558 restraints weight = 23848.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133083 restraints weight = 17727.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135586 restraints weight = 14979.341| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3466 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= 0.197 Angle : 0.708 12.621 23713 Z= 0.327 Chirality : 0.048 0.411 2923 Planarity : 0.003 0.050 2834 Dihedral : 9.278 58.903 4200 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.89 % Allowed : 15.88 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1931 helix: 0.69 (0.28), residues: 378 sheet: -0.05 (0.22), residues: 537 loop : -0.71 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 112 HIS 0.006 0.001 HIS C 352 PHE 0.016 0.002 PHE C 53 TYR 0.015 0.002 TYR G 191 ARG 0.007 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 58) link_NAG-ASN : angle 2.59179 ( 174) link_ALPHA1-6 : bond 0.00722 ( 4) link_ALPHA1-6 : angle 1.59573 ( 12) link_BETA1-4 : bond 0.00475 ( 32) link_BETA1-4 : angle 1.51131 ( 96) link_ALPHA1-2 : bond 0.00332 ( 4) link_ALPHA1-2 : angle 1.86052 ( 12) link_ALPHA1-3 : bond 0.01293 ( 4) link_ALPHA1-3 : angle 2.06398 ( 12) hydrogen bonds : bond 0.04634 ( 493) hydrogen bonds : angle 4.98180 ( 1329) SS BOND : bond 0.00470 ( 37) SS BOND : angle 1.75194 ( 74) covalent geometry : bond 0.00475 (17188) covalent geometry : angle 0.65923 (23333) *********************** 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 256 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8626 (p90) cc_final: 0.8239 (p90) REVERT: L 31 ASN cc_start: 0.8304 (p0) cc_final: 0.7943 (p0) REVERT: A 601 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8247 (mtmm) REVERT: A 615 SER cc_start: 0.8501 (t) cc_final: 0.8220 (m) REVERT: C 161 MET cc_start: 0.8451 (tpt) cc_final: 0.8171 (mmm) REVERT: F 540 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: F 621 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7205 (tm-30) REVERT: G 112 TRP cc_start: 0.8233 (t-100) cc_final: 0.7877 (t60) REVERT: G 217 TYR cc_start: 0.8260 (m-80) cc_final: 0.7374 (m-80) REVERT: G 475 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7310 (ptm) REVERT: I 38 VAL cc_start: 0.9150 (p) cc_final: 0.8908 (m) REVERT: I 104 MET cc_start: 0.8577 (ttt) cc_final: 0.8316 (ttt) REVERT: I 474 ASP cc_start: 0.6156 (t0) cc_final: 0.5889 (t0) outliers start: 50 outliers final: 35 residues processed: 235 average time/residue: 0.2648 time to fit residues: 96.3127 Evaluate side-chains 231 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 48 ILE 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 620 SER Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE 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 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 583 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 172 optimal weight: 0.8980 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.162716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130416 restraints weight = 23870.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131901 restraints weight = 18507.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133486 restraints weight = 15393.079| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17327 Z= 0.216 Angle : 0.719 12.011 23713 Z= 0.331 Chirality : 0.048 0.427 2923 Planarity : 0.003 0.041 2834 Dihedral : 8.934 59.124 4200 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.52 % Allowed : 16.22 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1931 helix: 0.35 (0.28), residues: 396 sheet: -0.15 (0.23), residues: 525 loop : -0.82 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 69 HIS 0.006 0.001 HIS C 352 PHE 0.017 0.002 PHE C 53 TYR 0.021 0.002 TYR L 87 ARG 0.005 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 58) link_NAG-ASN : angle 2.60863 ( 174) link_ALPHA1-6 : bond 0.00686 ( 4) link_ALPHA1-6 : angle 1.57886 ( 12) link_BETA1-4 : bond 0.00469 ( 32) link_BETA1-4 : angle 1.52187 ( 96) link_ALPHA1-2 : bond 0.00291 ( 4) link_ALPHA1-2 : angle 1.91093 ( 12) link_ALPHA1-3 : bond 0.01194 ( 4) link_ALPHA1-3 : angle 2.00065 ( 12) hydrogen bonds : bond 0.04640 ( 493) hydrogen bonds : angle 5.01313 ( 1329) SS BOND : bond 0.00288 ( 37) SS BOND : angle 1.83057 ( 74) covalent geometry : bond 0.00524 (17188) covalent geometry : angle 0.67060 (23333) *********************** 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 265 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 31 ASN cc_start: 0.8425 (p0) cc_final: 0.8098 (p0) REVERT: A 601 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8292 (mtmm) REVERT: C 161 MET cc_start: 0.8437 (tpt) cc_final: 0.8179 (mmm) REVERT: F 540 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: G 111 LEU cc_start: 0.8897 (mt) cc_final: 0.8642 (mt) REVERT: G 112 TRP cc_start: 0.8278 (t-100) cc_final: 0.8009 (t60) REVERT: G 217 TYR cc_start: 0.8385 (m-80) cc_final: 0.7597 (m-80) REVERT: G 322 ILE cc_start: 0.8879 (mm) cc_final: 0.8556 (mt) REVERT: G 475 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7240 (ptm) REVERT: I 38 VAL cc_start: 0.9163 (p) cc_final: 0.8895 (m) outliers start: 61 outliers final: 48 residues processed: 246 average time/residue: 0.2698 time to fit residues: 103.2550 Evaluate side-chains 239 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 52 HIS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 GLU 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 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 ILE 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 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 660 LEU 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 583 VAL 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 342 LEU Chi-restraints excluded: chain G residue 424 ILE 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 Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN F 630 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130490 restraints weight = 23839.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133441 restraints weight = 18148.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136243 restraints weight = 14517.865| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17327 Z= 0.136 Angle : 0.653 11.232 23713 Z= 0.300 Chirality : 0.046 0.400 2923 Planarity : 0.003 0.039 2834 Dihedral : 8.458 58.336 4200 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.89 % Allowed : 17.55 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1931 helix: 0.55 (0.28), residues: 396 sheet: -0.07 (0.22), residues: 537 loop : -0.74 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 338 HIS 0.004 0.001 HIS C 249 PHE 0.016 0.001 PHE C 53 TYR 0.012 0.001 TYR I 191 ARG 0.005 0.000 ARG L 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 58) link_NAG-ASN : angle 2.42405 ( 174) link_ALPHA1-6 : bond 0.00754 ( 4) link_ALPHA1-6 : angle 1.59975 ( 12) link_BETA1-4 : bond 0.00452 ( 32) link_BETA1-4 : angle 1.49076 ( 96) link_ALPHA1-2 : bond 0.00337 ( 4) link_ALPHA1-2 : angle 1.75162 ( 12) link_ALPHA1-3 : bond 0.01267 ( 4) link_ALPHA1-3 : angle 1.74065 ( 12) hydrogen bonds : bond 0.03956 ( 493) hydrogen bonds : angle 4.75112 ( 1329) SS BOND : bond 0.00255 ( 37) SS BOND : angle 1.53340 ( 74) covalent geometry : bond 0.00319 (17188) covalent geometry : angle 0.60672 (23333) *********************** 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 255 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8619 (p90) cc_final: 0.8391 (p90) REVERT: L 31 ASN cc_start: 0.8547 (p0) cc_final: 0.8092 (p0) REVERT: A 601 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8210 (mtmm) REVERT: C 161 MET cc_start: 0.8358 (tpt) cc_final: 0.8101 (mmm) REVERT: F 540 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: G 49 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: G 112 TRP cc_start: 0.8207 (t-100) cc_final: 0.7992 (t60) REVERT: G 217 TYR cc_start: 0.8355 (m-80) cc_final: 0.7580 (m-80) REVERT: G 322 ILE cc_start: 0.8843 (mm) cc_final: 0.8542 (mt) REVERT: G 475 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7057 (ptm) REVERT: I 38 VAL cc_start: 0.9024 (p) cc_final: 0.8775 (m) outliers start: 50 outliers final: 37 residues processed: 237 average time/residue: 0.2572 time to fit residues: 94.8945 Evaluate side-chains 231 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 L residue 48 ILE 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 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 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 49 GLU 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 342 LEU Chi-restraints excluded: chain G residue 424 ILE 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 Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 111 optimal weight: 1.9990 chunk 187 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 139 optimal weight: 0.0670 chunk 126 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 103 GLN F 630 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129193 restraints weight = 23819.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133152 restraints weight = 18574.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135559 restraints weight = 14359.529| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3970 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= 0.148 Angle : 0.663 11.145 23713 Z= 0.305 Chirality : 0.046 0.402 2923 Planarity : 0.003 0.042 2834 Dihedral : 8.233 58.381 4200 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.18 % Allowed : 17.84 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1931 helix: 0.59 (0.28), residues: 396 sheet: -0.05 (0.22), residues: 537 loop : -0.71 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 69 HIS 0.004 0.001 HIS C 249 PHE 0.015 0.001 PHE C 53 TYR 0.012 0.001 TYR I 173 ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 58) link_NAG-ASN : angle 2.36181 ( 174) link_ALPHA1-6 : bond 0.00694 ( 4) link_ALPHA1-6 : angle 1.59774 ( 12) link_BETA1-4 : bond 0.00458 ( 32) link_BETA1-4 : angle 1.47459 ( 96) link_ALPHA1-2 : bond 0.00335 ( 4) link_ALPHA1-2 : angle 1.75437 ( 12) link_ALPHA1-3 : bond 0.01140 ( 4) link_ALPHA1-3 : angle 1.72801 ( 12) hydrogen bonds : bond 0.03956 ( 493) hydrogen bonds : angle 4.71616 ( 1329) SS BOND : bond 0.00264 ( 37) SS BOND : angle 1.62620 ( 74) covalent geometry : bond 0.00353 (17188) covalent geometry : angle 0.61887 (23333) *********************** 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 251 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8624 (p90) cc_final: 0.8114 (p90) REVERT: L 31 ASN cc_start: 0.8584 (p0) cc_final: 0.8097 (p0) REVERT: A 542 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8200 (ttp-170) REVERT: A 601 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8191 (mtmm) REVERT: C 161 MET cc_start: 0.8384 (tpt) cc_final: 0.8140 (mmm) REVERT: C 428 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7690 (mm-40) REVERT: F 540 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: F 648 GLU cc_start: 0.7303 (pm20) cc_final: 0.7093 (pm20) REVERT: G 49 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: G 112 TRP cc_start: 0.8210 (t-100) cc_final: 0.7994 (t60) REVERT: G 217 TYR cc_start: 0.8362 (m-80) cc_final: 0.7599 (m-80) REVERT: G 322 ILE cc_start: 0.8843 (mm) cc_final: 0.8560 (mt) REVERT: G 475 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6927 (ptm) REVERT: I 38 VAL cc_start: 0.9023 (p) cc_final: 0.8760 (m) REVERT: I 104 MET cc_start: 0.8535 (ttt) cc_final: 0.8292 (ttt) outliers start: 55 outliers final: 42 residues processed: 232 average time/residue: 0.2720 time to fit residues: 97.4460 Evaluate side-chains 236 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 55 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE 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 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 B residue 660 LEU Chi-restraints excluded: chain C residue 36 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 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 49 GLU 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 348 GLN Chi-restraints excluded: chain G residue 424 ILE 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 Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 185 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN F 630 GLN F 640 GLN G 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127482 restraints weight = 23684.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130595 restraints weight = 17625.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.133500 restraints weight = 13809.859| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17327 Z= 0.186 Angle : 0.687 10.758 23713 Z= 0.318 Chirality : 0.047 0.414 2923 Planarity : 0.003 0.047 2834 Dihedral : 8.209 59.159 4200 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.83 % Allowed : 18.30 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1931 helix: 0.40 (0.28), residues: 408 sheet: -0.09 (0.23), residues: 525 loop : -0.79 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 69 HIS 0.005 0.001 HIS C 352 PHE 0.015 0.002 PHE C 53 TYR 0.014 0.002 TYR I 191 ARG 0.005 0.000 ARG G 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 58) link_NAG-ASN : angle 2.37711 ( 174) link_ALPHA1-6 : bond 0.00643 ( 4) link_ALPHA1-6 : angle 1.59533 ( 12) link_BETA1-4 : bond 0.00462 ( 32) link_BETA1-4 : angle 1.48409 ( 96) link_ALPHA1-2 : bond 0.00322 ( 4) link_ALPHA1-2 : angle 1.81917 ( 12) link_ALPHA1-3 : bond 0.01111 ( 4) link_ALPHA1-3 : angle 1.84379 ( 12) hydrogen bonds : bond 0.04217 ( 493) hydrogen bonds : angle 4.79428 ( 1329) SS BOND : bond 0.00309 ( 37) SS BOND : angle 1.68492 ( 74) covalent geometry : bond 0.00448 (17188) covalent geometry : angle 0.64414 (23333) *********************** 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 245 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8658 (p90) cc_final: 0.8117 (p90) REVERT: L 31 ASN cc_start: 0.8599 (p0) cc_final: 0.8181 (p0) REVERT: L 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.8366 (m-80) REVERT: A 542 ARG cc_start: 0.8460 (ttp-170) cc_final: 0.8246 (ttp-170) REVERT: A 601 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8228 (mtmm) REVERT: A 626 MET cc_start: 0.8196 (mtp) cc_final: 0.7818 (mtp) REVERT: C 161 MET cc_start: 0.8437 (tpt) cc_final: 0.8199 (mmm) REVERT: C 428 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7650 (mm-40) REVERT: F 540 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: F 648 GLU cc_start: 0.7286 (pm20) cc_final: 0.7084 (pm20) REVERT: G 217 TYR cc_start: 0.8467 (m-80) cc_final: 0.7755 (m-80) REVERT: G 322 ILE cc_start: 0.8874 (mm) cc_final: 0.8612 (mt) REVERT: G 475 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7058 (ptm) REVERT: I 38 VAL cc_start: 0.9023 (p) cc_final: 0.8759 (m) outliers start: 49 outliers final: 45 residues processed: 228 average time/residue: 0.2572 time to fit residues: 91.6407 Evaluate side-chains 239 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 52 HIS Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 622 ILE 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 636 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 36 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 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 F residue 638 TYR 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 342 LEU Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 424 ILE 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 Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 151 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 99 ASN C 103 GLN F 543 ASN F 630 GLN F 640 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.165982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129972 restraints weight = 23835.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132258 restraints weight = 18116.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135157 restraints weight = 15060.146| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17327 Z= 0.138 Angle : 0.660 10.267 23713 Z= 0.304 Chirality : 0.046 0.399 2923 Planarity : 0.003 0.065 2834 Dihedral : 8.052 58.494 4200 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.66 % Allowed : 18.76 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 1931 helix: 0.58 (0.28), residues: 396 sheet: -0.03 (0.23), residues: 525 loop : -0.75 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 69 HIS 0.004 0.001 HIS C 249 PHE 0.015 0.001 PHE C 53 TYR 0.011 0.001 TYR I 173 ARG 0.004 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 58) link_NAG-ASN : angle 2.28724 ( 174) link_ALPHA1-6 : bond 0.00684 ( 4) link_ALPHA1-6 : angle 1.60008 ( 12) link_BETA1-4 : bond 0.00454 ( 32) link_BETA1-4 : angle 1.47854 ( 96) link_ALPHA1-2 : bond 0.00351 ( 4) link_ALPHA1-2 : angle 1.75579 ( 12) link_ALPHA1-3 : bond 0.01085 ( 4) link_ALPHA1-3 : angle 1.69181 ( 12) hydrogen bonds : bond 0.03893 ( 493) hydrogen bonds : angle 4.71356 ( 1329) SS BOND : bond 0.00281 ( 37) SS BOND : angle 1.48120 ( 74) covalent geometry : bond 0.00328 (17188) covalent geometry : angle 0.61945 (23333) ********************** 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 250 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8606 (p90) cc_final: 0.8111 (p90) REVERT: L 31 ASN cc_start: 0.8607 (p0) cc_final: 0.8173 (p0) REVERT: L 32 TYR cc_start: 0.8561 (m-80) cc_final: 0.8336 (m-80) REVERT: A 601 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8196 (mtmm) REVERT: A 626 MET cc_start: 0.8171 (mtp) cc_final: 0.7797 (mtp) REVERT: C 161 MET cc_start: 0.8410 (tpt) cc_final: 0.8165 (mmm) REVERT: C 428 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7641 (mm-40) REVERT: F 540 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: G 112 TRP cc_start: 0.8241 (t-100) cc_final: 0.7982 (t60) REVERT: G 217 TYR cc_start: 0.8452 (m-80) cc_final: 0.7695 (m-80) REVERT: G 322 ILE cc_start: 0.8866 (mm) cc_final: 0.8609 (mt) REVERT: G 475 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7002 (ptm) REVERT: I 38 VAL cc_start: 0.9051 (p) cc_final: 0.8775 (m) REVERT: I 370 GLU cc_start: 0.7940 (mp0) cc_final: 0.7733 (mp0) outliers start: 46 outliers final: 40 residues processed: 233 average time/residue: 0.2614 time to fit residues: 95.2500 Evaluate side-chains 237 residues out of total 1735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 55 THR 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 73 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 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 B residue 660 LEU Chi-restraints excluded: chain C residue 36 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 528 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 638 TYR 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 424 ILE 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 Chi-restraints excluded: chain I residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 0.0270 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN F 630 GLN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.166698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130049 restraints weight = 23806.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133334 restraints weight = 18141.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135049 restraints weight = 14759.543| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17327 Z= 0.129 Angle : 0.649 10.170 23713 Z= 0.300 Chirality : 0.046 0.392 2923 Planarity : 0.003 0.059 2834 Dihedral : 7.876 59.282 4200 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.37 % Allowed : 19.05 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1931 helix: 0.65 (0.28), residues: 396 sheet: -0.02 (0.22), residues: 543 loop : -0.71 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 36 HIS 0.004 0.001 HIS C 249 PHE 0.015 0.001 PHE C 53 TYR 0.012 0.001 TYR C 484 ARG 0.011 0.000 ARG A 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 58) link_NAG-ASN : angle 2.21570 ( 174) link_ALPHA1-6 : bond 0.00697 ( 4) link_ALPHA1-6 : angle 1.61533 ( 12) link_BETA1-4 : bond 0.00458 ( 32) link_BETA1-4 : angle 1.46678 ( 96) link_ALPHA1-2 : bond 0.00355 ( 4) link_ALPHA1-2 : angle 1.70468 ( 12) link_ALPHA1-3 : bond 0.01034 ( 4) link_ALPHA1-3 : angle 1.63410 ( 12) hydrogen bonds : bond 0.03709 ( 493) hydrogen bonds : angle 4.63656 ( 1329) SS BOND : bond 0.00272 ( 37) SS BOND : angle 1.39412 ( 74) covalent geometry : bond 0.00304 (17188) covalent geometry : angle 0.61005 (23333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.78 seconds wall clock time: 85 minutes 48.58 seconds (5148.58 seconds total)