Starting phenix.real_space_refine on Sat Aug 8 04:12:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.map" model { file = "/net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymk_73109/08_2026/9ymk_73109.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 15798 2.51 5 N 4209 2.21 5 O 5124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25272 Number of models: 1 Model: "" Number of chains: 39 Chain: "G" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3457 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Chain: "B" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 976 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3457 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 976 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 934 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3457 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 956 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "P" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 976 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "R" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} 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 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "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: 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 Time building chain proxies: 6.16, per 1000 atoms: 0.24 Number of scatterers: 25272 At special positions: 0 Unit cell: (155.085, 163.356, 169.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 5124 8.00 N 4209 7.00 C 15798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN d 5 " - " MAN d 6 " " MAN d 8 " - " MAN d 9 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 8 " " MAN T 4 " - " MAN T 7 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 8 " " MAN Y 4 " - " MAN Y 7 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 8 " " MAN d 4 " - " MAN d 7 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA X 3 " - " MAN X 7 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 4 " - " MAN Y 5 " " BMA c 3 " - " MAN c 7 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 448 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 355 " " NAG A 607 " - " ASN A 160 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 88 " " NAG A 610 " - " ASN A 276 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 448 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 355 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 301 " " NAG C 609 " - " ASN C 88 " " NAG C 610 " - " ASN C 276 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 448 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 355 " " NAG E 607 " - " ASN E 160 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 88 " " NAG E 610 " - " ASN E 276 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 611 " " NAG S 1 " - " ASN A 392 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN C 392 " " NAG Y 1 " - " ASN C 332 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 262 " " NAG b 1 " - " ASN C 386 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 156 " " NAG f 1 " - " ASN E 262 " " NAG g 1 " - " ASN E 386 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5646 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 48 sheets defined 17.0% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.566A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.610A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.025A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.092A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.414A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.807A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.881A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.634A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100 through 100D Processing helix chain 'L' and resid 27B through 31 removed outlier: 3.785A pdb=" N GLU L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.566A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.610A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.093A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.414A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.807A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.881A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 661 removed outlier: 3.634A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 31 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 100 through 100D Processing helix chain 'N' and resid 27B through 31 removed outlier: 3.785A pdb=" N GLU N 31 " --> pdb=" O ILE N 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.566A pdb=" N SER O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.610A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.748A pdb=" N THR O 87 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 115 removed outlier: 4.024A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.092A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.414A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.807A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.881A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.635A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 31 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100 through 100D Processing helix chain 'R' and resid 27B through 31 removed outlier: 3.785A pdb=" N GLU R 31 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.609A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.961A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AA5, first strand: chain 'I' and resid 45 through 48 removed outlier: 5.655A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.355A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.735A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA9, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB1, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.987A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 3.791A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.559A pdb=" N GLN H 5 " --> pdb=" O ASP H 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.586A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.513A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.608A pdb=" N LEU J 80 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.961A pdb=" N VAL J 12 " --> pdb=" O THR J 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AC3, first strand: chain 'M' and resid 45 through 48 removed outlier: 5.655A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE M 48 " --> pdb=" O TRP M 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.355A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.735A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.988A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 3.791A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.560A pdb=" N GLN K 5 " --> pdb=" O ASP K 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 33 through 39 removed outlier: 6.586A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 102 through 103 Processing sheet with id=AD3, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'N' and resid 20 through 24 Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.514A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 3 through 5 removed outlier: 3.608A pdb=" N LEU O 80 " --> pdb=" O LEU O 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.961A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.664A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 18 through 24 Processing sheet with id=AE1, first strand: chain 'Q' and resid 45 through 48 removed outlier: 5.655A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 37 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN Q 37 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE Q 48 " --> pdb=" O TRP Q 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.355A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.734A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AE5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AE6, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.987A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 3.791A pdb=" N ASP E 322 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AE8, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.559A pdb=" N GLN P 5 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 33 through 39 removed outlier: 6.586A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 102 through 103 Processing sheet with id=AF1, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.692A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'R' and resid 20 through 24 Processing sheet with id=AF3, first strand: chain 'R' and resid 53 through 54 removed outlier: 6.513A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7806 1.34 - 1.46: 6603 1.46 - 1.59: 11190 1.59 - 1.71: 0 1.71 - 1.83: 189 Bond restraints: 25788 Sorted by residual: bond pdb=" C1 BMA a 3 " pdb=" C2 BMA a 3 " ideal model delta sigma weight residual 1.519 1.579 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" N GLU N 1 " pdb=" CA GLU N 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLU L 1 " pdb=" CA GLU L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 25783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 33099 2.00 - 4.00: 1596 4.00 - 6.00: 255 6.00 - 8.00: 54 8.00 - 10.00: 9 Bond angle restraints: 35013 Sorted by residual: angle pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 114.40 122.95 -8.55 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " ideal model delta sigma weight residual 114.40 122.93 -8.53 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " ideal model delta sigma weight residual 114.40 122.92 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CB MET I 47 " pdb=" CG MET I 47 " pdb=" SD MET I 47 " ideal model delta sigma weight residual 112.70 122.70 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB MET M 47 " pdb=" CG MET M 47 " pdb=" SD MET M 47 " ideal model delta sigma weight residual 112.70 122.70 -10.00 3.00e+00 1.11e-01 1.11e+01 ... (remaining 35008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 14849 20.31 - 40.63: 1347 40.63 - 60.94: 346 60.94 - 81.25: 78 81.25 - 101.56: 39 Dihedral angle restraints: 16659 sinusoidal: 7851 harmonic: 8808 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -42.12 -43.88 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -42.13 -43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -42.14 -43.86 1 1.00e+01 1.00e-02 2.68e+01 ... (remaining 16656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3363 0.061 - 0.122: 689 0.122 - 0.182: 145 0.182 - 0.243: 21 0.243 - 0.304: 6 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 4221 not shown) Planarity restraints: 4365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 96 " 0.366 9.50e-02 1.11e+02 1.65e-01 1.97e+01 pdb=" NE ARG P 96 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG P 96 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG P 96 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG P 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 96 " 0.367 9.50e-02 1.11e+02 1.65e-01 1.96e+01 pdb=" NE ARG K 96 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG K 96 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG K 96 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 96 " 0.366 9.50e-02 1.11e+02 1.65e-01 1.96e+01 pdb=" NE ARG H 96 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG H 96 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG H 96 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG H 96 " 0.003 2.00e-02 2.50e+03 ... (remaining 4362 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 9181 2.89 - 3.39: 22191 3.39 - 3.90: 43369 3.90 - 4.40: 52025 4.40 - 4.90: 85784 Nonbonded interactions: 212550 Sorted by model distance: nonbonded pdb=" O5 MAN X 5 " pdb=" O6 MAN X 5 " model vdw 2.388 2.432 nonbonded pdb=" O5 MAN c 5 " pdb=" O6 MAN c 5 " model vdw 2.388 2.432 nonbonded pdb=" O5 MAN S 5 " pdb=" O6 MAN S 5 " model vdw 2.388 2.432 nonbonded pdb=" O5 MAN d 8 " pdb=" O6 MAN d 8 " model vdw 2.390 2.432 nonbonded pdb=" O5 MAN T 8 " pdb=" O6 MAN T 8 " model vdw 2.390 2.432 ... (remaining 212545 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'c' } ncs_group { reference = chain 'T' selection = chain 'Y' selection = chain 'd' } ncs_group { reference = chain 'U' selection = chain 'W' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'V' selection = chain 'a' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.150 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 0.060 25938 Z= 0.226 Angle : 1.017 13.218 35418 Z= 0.496 Chirality : 0.054 0.304 4224 Planarity : 0.008 0.165 4314 Dihedral : 17.257 101.565 10878 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.11 % Allowed : 23.15 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3015 helix: -0.15 (0.26), residues: 414 sheet: -1.14 (0.16), residues: 915 loop : -1.26 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG P 96 TYR 0.023 0.002 TYR L 86 PHE 0.028 0.003 PHE K 57 TRP 0.017 0.002 TRP C 395 HIS 0.007 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.22 (25788) covalent geometry : angle 0.97505 / 0.49 (35013) SS BOND : bond 0.00832 / 0.55 ( 45) SS BOND : angle 1.19092 / 0.84 ( 90) hydrogen bonds : bond 0.12213 / 7.99 ( 687) hydrogen bonds : angle 6.46082 / 4.41 ( 1827) link_ALPHA1-2 : bond 0.00133 / 0.09 ( 12) link_ALPHA1-2 : angle 1.80898 / 1.14 ( 36) link_ALPHA1-3 : bond 0.00302 / 0.18 ( 9) link_ALPHA1-3 : angle 1.98072 / 1.20 ( 27) link_ALPHA1-6 : bond 0.00563 / 0.28 ( 9) link_ALPHA1-6 : angle 2.39600 / 1.33 ( 27) link_BETA1-4 : bond 0.01608 / 0.68 ( 24) link_BETA1-4 : angle 3.57649 / 2.66 ( 72) link_NAG-ASN : bond 0.00461 / 0.35 ( 51) link_NAG-ASN : angle 3.55473 / 2.39 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 473 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 91 TYR cc_start: 0.7747 (m-80) cc_final: 0.7533 (m-80) REVERT: G 105 GLN cc_start: 0.6975 (mm110) cc_final: 0.6470 (mp10) REVERT: I 53 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7767 (mm-40) REVERT: A 117 LYS cc_start: 0.8445 (mttt) cc_final: 0.8208 (mttt) REVERT: A 140 ASP cc_start: 0.8302 (m-30) cc_final: 0.8071 (m-30) REVERT: A 169 LYS cc_start: 0.7637 (mtmt) cc_final: 0.7371 (mmtm) REVERT: A 232 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7536 (mmmt) REVERT: A 308 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7860 (mtp180) REVERT: A 322 ASP cc_start: 0.8145 (p0) cc_final: 0.7882 (t70) REVERT: A 370 GLU cc_start: 0.8202 (mp0) cc_final: 0.7992 (mp0) REVERT: A 371 VAL cc_start: 0.8747 (m) cc_final: 0.8368 (p) REVERT: B 633 LYS cc_start: 0.7974 (mttt) cc_final: 0.7367 (mtmp) REVERT: B 655 LYS cc_start: 0.8231 (tptm) cc_final: 0.7723 (tptt) REVERT: H 72 ASP cc_start: 0.7772 (t0) cc_final: 0.7568 (t0) REVERT: H 77 GLN cc_start: 0.7482 (tt0) cc_final: 0.7143 (tm-30) REVERT: L 53 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7236 (mp10) REVERT: L 63 SER cc_start: 0.7960 (t) cc_final: 0.7350 (p) REVERT: L 74 VAL cc_start: 0.7682 (t) cc_final: 0.7287 (m) REVERT: J 32 PHE cc_start: 0.8545 (m-80) cc_final: 0.8318 (m-10) REVERT: J 105 GLN cc_start: 0.7261 (mm110) cc_final: 0.6950 (mp-120) REVERT: M 14 SER cc_start: 0.5924 (m) cc_final: 0.5724 (t) REVERT: M 47 MET cc_start: 0.8114 (mmm) cc_final: 0.7788 (mmm) REVERT: M 53 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7619 (mm-40) REVERT: M 65 SER cc_start: 0.8578 (t) cc_final: 0.7957 (p) REVERT: C 82 GLN cc_start: 0.7448 (mm110) cc_final: 0.7104 (tp-100) REVERT: C 95 MET cc_start: 0.8850 (ptm) cc_final: 0.8632 (ptm) REVERT: C 106 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6947 (mm-30) REVERT: C 114 GLN cc_start: 0.7837 (mt0) cc_final: 0.7149 (mm110) REVERT: C 117 LYS cc_start: 0.8416 (mttt) cc_final: 0.8112 (mttt) REVERT: C 140 ASP cc_start: 0.8437 (m-30) cc_final: 0.8132 (m-30) REVERT: C 169 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7359 (mmtm) REVERT: C 232 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7989 (mtmt) REVERT: C 396 ILE cc_start: 0.7311 (pt) cc_final: 0.6908 (mm) REVERT: D 633 LYS cc_start: 0.7992 (mttt) cc_final: 0.7486 (mtpt) REVERT: D 648 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7951 (mt-10) REVERT: D 652 GLN cc_start: 0.8411 (mt0) cc_final: 0.8146 (mt0) REVERT: D 655 LYS cc_start: 0.8346 (tptm) cc_final: 0.8123 (tptt) REVERT: K 77 GLN cc_start: 0.7283 (tt0) cc_final: 0.6960 (tm-30) REVERT: N 52 ASN cc_start: 0.7166 (p0) cc_final: 0.6962 (p0) REVERT: N 63 SER cc_start: 0.8166 (t) cc_final: 0.7538 (p) REVERT: N 74 VAL cc_start: 0.7798 (t) cc_final: 0.7436 (m) REVERT: O 34 MET cc_start: 0.8717 (mmm) cc_final: 0.8499 (mtp) REVERT: O 67 PHE cc_start: 0.7839 (m-80) cc_final: 0.7604 (m-10) REVERT: Q 47 MET cc_start: 0.8132 (mmm) cc_final: 0.7905 (mmp) REVERT: Q 65 SER cc_start: 0.8588 (t) cc_final: 0.8015 (p) REVERT: Q 95 GLN cc_start: 0.7374 (mp10) cc_final: 0.6942 (mm110) REVERT: E 106 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6767 (mm-30) REVERT: E 121 LYS cc_start: 0.8579 (mttt) cc_final: 0.8251 (mmpt) REVERT: E 125 LEU cc_start: 0.8783 (tp) cc_final: 0.8360 (mm) REVERT: E 140 ASP cc_start: 0.8374 (m-30) cc_final: 0.8174 (m-30) REVERT: E 169 LYS cc_start: 0.7608 (mtmt) cc_final: 0.7188 (mptt) REVERT: E 232 LYS cc_start: 0.8390 (mtpp) cc_final: 0.8189 (mtpt) REVERT: E 370 GLU cc_start: 0.8194 (mp0) cc_final: 0.7891 (mp0) REVERT: E 504 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.6435 (tpp-160) REVERT: F 588 ARG cc_start: 0.8524 (mtm110) cc_final: 0.8310 (mtm110) REVERT: F 633 LYS cc_start: 0.7950 (mttt) cc_final: 0.7374 (mtmp) REVERT: F 648 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F 655 LYS cc_start: 0.8385 (tptm) cc_final: 0.7968 (tptt) REVERT: P 77 GLN cc_start: 0.7370 (tt0) cc_final: 0.6758 (tm-30) REVERT: R 52 ASN cc_start: 0.7255 (p0) cc_final: 0.6831 (p0) REVERT: R 53 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7001 (mp10) REVERT: R 63 SER cc_start: 0.8029 (t) cc_final: 0.7355 (p) REVERT: R 74 VAL cc_start: 0.7543 (t) cc_final: 0.7324 (m) outliers start: 3 outliers final: 0 residues processed: 476 average time/residue: 0.6188 time to fit residues: 341.4594 Evaluate side-chains 389 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 114 GLN A 216 HIS B 543 ASN B 616 ASN B 653 GLN H 39 GLN H 58 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS J 105 GLN ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN C 98 ASN C 216 HIS C 280 ASN C 352 HIS D 540 GLN K 39 GLN K 58 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS ** Q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 ASN E 114 GLN E 216 HIS F 540 GLN F 543 ASN F 653 GLN P 39 GLN P 58 HIS ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110994 restraints weight = 28254.877| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.96 r_work: 0.3138 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25938 Z= 0.303 Angle : 0.812 10.897 35418 Z= 0.387 Chirality : 0.051 0.259 4224 Planarity : 0.006 0.052 4314 Dihedral : 10.543 75.815 5421 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.31 % Allowed : 20.97 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3015 helix: 0.15 (0.25), residues: 402 sheet: -0.78 (0.17), residues: 930 loop : -1.05 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 94 TYR 0.016 0.002 TYR C 217 PHE 0.024 0.003 PHE J 29 TRP 0.018 0.003 TRP E 35 HIS 0.005 0.001 HIS P 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.30 (25788) covalent geometry : angle 0.75230 / 0.37 (35013) SS BOND : bond 0.00543 / 0.38 ( 45) SS BOND : angle 1.37208 / 0.94 ( 90) hydrogen bonds : bond 0.04785 / 3.21 ( 687) hydrogen bonds : angle 5.52070 / 3.76 ( 1827) link_ALPHA1-2 : bond 0.00470 / 0.24 ( 12) link_ALPHA1-2 : angle 2.40977 / 1.52 ( 36) link_ALPHA1-3 : bond 0.00591 / 0.38 ( 9) link_ALPHA1-3 : angle 1.63595 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00148 / 0.09 ( 9) link_ALPHA1-6 : angle 1.77843 / 1.15 ( 27) link_BETA1-4 : bond 0.00689 / 0.36 ( 24) link_BETA1-4 : angle 2.96197 / 2.08 ( 72) link_NAG-ASN : bond 0.00827 / 0.60 ( 51) link_NAG-ASN : angle 3.95421 / 2.59 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 386 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7182 (mm110) cc_final: 0.6809 (mp10) REVERT: I 45 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7289 (ttpt) REVERT: I 53 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7912 (mm-40) REVERT: A 114 GLN cc_start: 0.7911 (mt0) cc_final: 0.7097 (mm110) REVERT: A 117 LYS cc_start: 0.8491 (mttt) cc_final: 0.8210 (mttt) REVERT: A 169 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7550 (mmtm) REVERT: A 232 LYS cc_start: 0.8666 (mtpp) cc_final: 0.7723 (mmtm) REVERT: A 322 ASP cc_start: 0.8171 (p0) cc_final: 0.7891 (t70) REVERT: B 633 LYS cc_start: 0.8060 (mttt) cc_final: 0.7501 (mtmp) REVERT: B 652 GLN cc_start: 0.8613 (mt0) cc_final: 0.8391 (mt0) REVERT: L 53 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7486 (mp10) REVERT: L 63 SER cc_start: 0.8024 (t) cc_final: 0.7721 (m) REVERT: J 94 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8410 (p) REVERT: J 105 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6991 (mp10) REVERT: M 53 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7816 (mm-40) REVERT: C 95 MET cc_start: 0.9054 (ptm) cc_final: 0.8843 (ptm) REVERT: C 114 GLN cc_start: 0.7987 (mt0) cc_final: 0.7170 (mm110) REVERT: C 117 LYS cc_start: 0.8486 (mttt) cc_final: 0.7956 (mmpt) REVERT: C 140 ASP cc_start: 0.8602 (m-30) cc_final: 0.8398 (m-30) REVERT: C 169 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7436 (mmtm) REVERT: C 232 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8210 (mtmt) REVERT: C 396 ILE cc_start: 0.7396 (pt) cc_final: 0.7076 (mm) REVERT: D 535 MET cc_start: 0.8826 (mpp) cc_final: 0.8486 (mmt) REVERT: D 633 LYS cc_start: 0.8034 (mttt) cc_final: 0.7501 (mtpt) REVERT: D 652 GLN cc_start: 0.8697 (mt0) cc_final: 0.8448 (mt0) REVERT: K 100 ARG cc_start: 0.8735 (ptt180) cc_final: 0.8498 (ptt180) REVERT: N 52 ASN cc_start: 0.7446 (p0) cc_final: 0.7210 (p0) REVERT: N 63 SER cc_start: 0.8206 (t) cc_final: 0.7873 (m) REVERT: N 74 VAL cc_start: 0.7513 (t) cc_final: 0.7247 (m) REVERT: O 34 MET cc_start: 0.8839 (mmm) cc_final: 0.8465 (mtp) REVERT: O 94 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8367 (p) REVERT: O 105 GLN cc_start: 0.7209 (mm110) cc_final: 0.6812 (mp-120) REVERT: Q 14 SER cc_start: 0.6444 (OUTLIER) cc_final: 0.5972 (m) REVERT: Q 53 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8120 (mm110) REVERT: E 106 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6824 (mm-30) REVERT: E 114 GLN cc_start: 0.7784 (mt0) cc_final: 0.7100 (mm-40) REVERT: E 121 LYS cc_start: 0.8796 (mttt) cc_final: 0.8445 (mmpt) REVERT: E 125 LEU cc_start: 0.8802 (tp) cc_final: 0.8459 (mm) REVERT: E 140 ASP cc_start: 0.8446 (m-30) cc_final: 0.8223 (m-30) REVERT: E 169 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7367 (mptt) REVERT: E 232 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8327 (mtpp) REVERT: E 271 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8844 (mt) REVERT: E 322 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8225 (t70) REVERT: E 504 ARG cc_start: 0.6876 (tpp-160) cc_final: 0.6387 (tpm170) REVERT: F 535 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8575 (mtp) REVERT: F 543 ASN cc_start: 0.8512 (m-40) cc_final: 0.8292 (m110) REVERT: F 575 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: F 633 LYS cc_start: 0.8067 (mttt) cc_final: 0.7453 (mtpt) REVERT: P 66 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.5983 (mtm-85) REVERT: R 52 ASN cc_start: 0.7484 (p0) cc_final: 0.7262 (p0) REVERT: R 53 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7296 (mt0) REVERT: R 63 SER cc_start: 0.7941 (t) cc_final: 0.7509 (m) REVERT: R 74 VAL cc_start: 0.7490 (t) cc_final: 0.7226 (m) REVERT: R 95 TYR cc_start: 0.8391 (m-80) cc_final: 0.7984 (m-80) outliers start: 115 outliers final: 69 residues processed: 469 average time/residue: 0.5047 time to fit residues: 279.9316 Evaluate side-chains 447 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 370 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain R residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 131 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN I 69 ASN B 616 ASN H 39 GLN L 38 HIS M 31 ASN M 69 ASN M 79 GLN C 280 ASN D 540 GLN K 39 GLN N 38 HIS Q 31 ASN Q 69 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.157072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.112849 restraints weight = 28341.998| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.98 r_work: 0.3169 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25938 Z= 0.161 Angle : 0.661 8.776 35418 Z= 0.316 Chirality : 0.045 0.240 4224 Planarity : 0.004 0.048 4314 Dihedral : 9.511 71.961 5421 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.16 % Allowed : 21.80 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3015 helix: 0.58 (0.26), residues: 420 sheet: -0.54 (0.17), residues: 933 loop : -0.85 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 94 TYR 0.028 0.001 TYR M 49 PHE 0.019 0.002 PHE G 67 TRP 0.013 0.001 TRP F 610 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (25788) covalent geometry : angle 0.61034 / 0.30 (35013) SS BOND : bond 0.00408 / 0.29 ( 45) SS BOND : angle 1.32000 / 0.94 ( 90) hydrogen bonds : bond 0.03878 / 2.63 ( 687) hydrogen bonds : angle 5.11128 / 3.48 ( 1827) link_ALPHA1-2 : bond 0.00246 / 0.13 ( 12) link_ALPHA1-2 : angle 2.15820 / 1.37 ( 36) link_ALPHA1-3 : bond 0.00830 / 0.52 ( 9) link_ALPHA1-3 : angle 1.46018 / 0.86 ( 27) link_ALPHA1-6 : bond 0.00266 / 0.14 ( 9) link_ALPHA1-6 : angle 1.54122 / 0.96 ( 27) link_BETA1-4 : bond 0.00524 / 0.23 ( 24) link_BETA1-4 : angle 2.26921 / 1.57 ( 72) link_NAG-ASN : bond 0.00417 / 0.30 ( 51) link_NAG-ASN : angle 3.24048 / 2.14 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 366 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7181 (mm110) cc_final: 0.6851 (mp10) REVERT: I 30 TYR cc_start: 0.8692 (m-80) cc_final: 0.8421 (m-80) REVERT: I 45 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7392 (ttpt) REVERT: I 53 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7934 (mm-40) REVERT: I 88 CYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7527 (p) REVERT: A 114 GLN cc_start: 0.7966 (mt0) cc_final: 0.7229 (mm110) REVERT: A 117 LYS cc_start: 0.8485 (mttt) cc_final: 0.8189 (mttt) REVERT: A 140 ASP cc_start: 0.8413 (m-30) cc_final: 0.8193 (m-30) REVERT: A 232 LYS cc_start: 0.8668 (mtpp) cc_final: 0.7787 (mmtm) REVERT: A 308 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8195 (mtp180) REVERT: A 322 ASP cc_start: 0.8189 (p0) cc_final: 0.7927 (t70) REVERT: B 633 LYS cc_start: 0.8102 (mttt) cc_final: 0.7573 (mtmp) REVERT: L 52 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7007 (p0) REVERT: L 53 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7553 (mp10) REVERT: L 63 SER cc_start: 0.8043 (t) cc_final: 0.7527 (p) REVERT: L 67 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7527 (p) REVERT: J 32 PHE cc_start: 0.8606 (m-80) cc_final: 0.8307 (m-10) REVERT: J 105 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7127 (mp-120) REVERT: M 47 MET cc_start: 0.8476 (mmm) cc_final: 0.8132 (mmm) REVERT: M 53 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 95 MET cc_start: 0.9087 (ptm) cc_final: 0.8849 (ptm) REVERT: C 114 GLN cc_start: 0.7991 (mt0) cc_final: 0.7252 (mm110) REVERT: C 117 LYS cc_start: 0.8486 (mttt) cc_final: 0.7984 (mmpt) REVERT: C 140 ASP cc_start: 0.8540 (m-30) cc_final: 0.8322 (m-30) REVERT: C 169 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7435 (mmtm) REVERT: C 232 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8267 (mtmt) REVERT: C 327 ARG cc_start: 0.8801 (mtt-85) cc_final: 0.8577 (mtt-85) REVERT: C 396 ILE cc_start: 0.7238 (pt) cc_final: 0.6912 (mm) REVERT: D 535 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8525 (mmt) REVERT: D 633 LYS cc_start: 0.8082 (mttt) cc_final: 0.7579 (mtpt) REVERT: D 652 GLN cc_start: 0.8701 (mt0) cc_final: 0.8488 (mt0) REVERT: K 71 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7394 (pttm) REVERT: N 63 SER cc_start: 0.8227 (t) cc_final: 0.7613 (p) REVERT: N 74 VAL cc_start: 0.7512 (t) cc_final: 0.7182 (m) REVERT: O 21 SER cc_start: 0.7527 (m) cc_final: 0.7325 (t) REVERT: O 34 MET cc_start: 0.8793 (mmm) cc_final: 0.8517 (mtp) REVERT: O 105 GLN cc_start: 0.7183 (mm110) cc_final: 0.6951 (mp-120) REVERT: Q 14 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5913 (m) REVERT: Q 47 MET cc_start: 0.8423 (mmp) cc_final: 0.8138 (mmm) REVERT: Q 53 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8086 (mm110) REVERT: E 95 MET cc_start: 0.9184 (ptm) cc_final: 0.8908 (ptm) REVERT: E 106 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6932 (mm-30) REVERT: E 114 GLN cc_start: 0.7775 (mt0) cc_final: 0.7173 (mm-40) REVERT: E 125 LEU cc_start: 0.8817 (tp) cc_final: 0.8515 (mm) REVERT: E 169 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7425 (mptt) REVERT: E 232 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8352 (mtpp) REVERT: E 322 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8209 (t70) REVERT: E 504 ARG cc_start: 0.6931 (tpp-160) cc_final: 0.6477 (tpm170) REVERT: F 535 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8594 (mtp) REVERT: F 543 ASN cc_start: 0.8509 (m-40) cc_final: 0.8280 (m110) REVERT: F 633 LYS cc_start: 0.8122 (mttt) cc_final: 0.7561 (mtpt) REVERT: P 66 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6079 (mtm-85) REVERT: R 52 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7204 (p0) REVERT: R 53 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7284 (mt0) REVERT: R 63 SER cc_start: 0.7893 (t) cc_final: 0.7595 (m) outliers start: 111 outliers final: 49 residues processed: 445 average time/residue: 0.6212 time to fit residues: 322.6439 Evaluate side-chains 416 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 356 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain R residue 52 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 219 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 293 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN B 540 GLN B 616 ASN L 6 GLN L 38 HIS M 31 ASN C 98 ASN C 280 ASN D 540 GLN N 6 GLN Q 31 ASN E 422 GLN P 39 GLN R 6 GLN R 38 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.154295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109788 restraints weight = 28051.718| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.97 r_work: 0.3137 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 25938 Z= 0.284 Angle : 0.766 10.477 35418 Z= 0.364 Chirality : 0.049 0.247 4224 Planarity : 0.005 0.048 4314 Dihedral : 9.515 74.154 5421 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.28 % Allowed : 20.86 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3015 helix: 0.40 (0.25), residues: 420 sheet: -0.57 (0.16), residues: 936 loop : -0.84 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 94 TYR 0.026 0.002 TYR I 49 PHE 0.030 0.002 PHE O 67 TRP 0.014 0.002 TRP E 35 HIS 0.004 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.28 (25788) covalent geometry : angle 0.70315 / 0.35 (35013) SS BOND : bond 0.00574 / 0.39 ( 45) SS BOND : angle 1.89545 / 1.33 ( 90) hydrogen bonds : bond 0.04654 / 3.13 ( 687) hydrogen bonds : angle 5.20772 / 3.54 ( 1827) link_ALPHA1-2 : bond 0.00485 / 0.24 ( 12) link_ALPHA1-2 : angle 2.42805 / 1.54 ( 36) link_ALPHA1-3 : bond 0.00645 / 0.41 ( 9) link_ALPHA1-3 : angle 1.67265 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00172 / 0.11 ( 9) link_ALPHA1-6 : angle 1.71991 / 1.09 ( 27) link_BETA1-4 : bond 0.00582 / 0.30 ( 24) link_BETA1-4 : angle 2.62148 / 1.81 ( 72) link_NAG-ASN : bond 0.00743 / 0.53 ( 51) link_NAG-ASN : angle 3.86165 / 2.52 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 351 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7301 (mm110) cc_final: 0.6927 (mp10) REVERT: I 45 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7381 (ttpt) REVERT: I 53 GLN cc_start: 0.8245 (mm-40) cc_final: 0.8001 (mm-40) REVERT: I 69 ASN cc_start: 0.7980 (m-40) cc_final: 0.7737 (m110) REVERT: I 88 CYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7539 (p) REVERT: A 117 LYS cc_start: 0.8544 (mttt) cc_final: 0.8298 (mttt) REVERT: A 232 LYS cc_start: 0.8635 (mtpp) cc_final: 0.7746 (mmtm) REVERT: A 308 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8223 (mtp180) REVERT: B 633 LYS cc_start: 0.8119 (mttt) cc_final: 0.7586 (mtmp) REVERT: H 100 ARG cc_start: 0.8717 (ptt180) cc_final: 0.8503 (ptt90) REVERT: L 52 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7334 (p0) REVERT: L 53 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7555 (mp10) REVERT: L 63 SER cc_start: 0.8110 (t) cc_final: 0.7834 (m) REVERT: L 67 SER cc_start: 0.7767 (OUTLIER) cc_final: 0.7544 (p) REVERT: J 32 PHE cc_start: 0.8710 (m-80) cc_final: 0.8421 (m-10) REVERT: J 105 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7160 (mp-120) REVERT: M 47 MET cc_start: 0.8437 (mmm) cc_final: 0.7983 (mmm) REVERT: M 53 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7895 (mm-40) REVERT: C 95 MET cc_start: 0.9157 (ptm) cc_final: 0.8873 (ptm) REVERT: C 114 GLN cc_start: 0.8051 (mt0) cc_final: 0.7302 (mm110) REVERT: C 117 LYS cc_start: 0.8462 (mttt) cc_final: 0.8038 (mmpt) REVERT: C 129 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8500 (mt) REVERT: C 169 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7441 (mmtm) REVERT: C 232 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8240 (mtmt) REVERT: C 396 ILE cc_start: 0.7417 (pt) cc_final: 0.7084 (mm) REVERT: C 432 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: D 535 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: D 633 LYS cc_start: 0.8154 (mttt) cc_final: 0.7644 (mtpt) REVERT: D 652 GLN cc_start: 0.8733 (mt0) cc_final: 0.8524 (mt0) REVERT: K 71 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7425 (pttm) REVERT: N 52 ASN cc_start: 0.7596 (p0) cc_final: 0.7337 (p0) REVERT: N 63 SER cc_start: 0.8244 (t) cc_final: 0.7944 (m) REVERT: O 105 GLN cc_start: 0.7221 (mm110) cc_final: 0.6979 (mp-120) REVERT: Q 14 SER cc_start: 0.6458 (OUTLIER) cc_final: 0.5997 (m) REVERT: Q 47 MET cc_start: 0.8479 (mmp) cc_final: 0.8128 (mmm) REVERT: Q 53 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7969 (mm-40) REVERT: E 106 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6945 (mm-30) REVERT: E 114 GLN cc_start: 0.7814 (mt0) cc_final: 0.7180 (mm-40) REVERT: E 169 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7422 (mptt) REVERT: E 232 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8373 (mtpp) REVERT: E 322 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8252 (t70) REVERT: E 504 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6475 (tpm170) REVERT: F 535 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8618 (mtp) REVERT: F 575 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: F 633 LYS cc_start: 0.8138 (mttt) cc_final: 0.7571 (mtpt) REVERT: P 66 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.5903 (mtm-85) REVERT: R 52 ASN cc_start: 0.7619 (p0) cc_final: 0.7389 (p0) REVERT: R 53 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7254 (mt0) REVERT: R 63 SER cc_start: 0.7910 (t) cc_final: 0.7637 (m) outliers start: 141 outliers final: 86 residues processed: 455 average time/residue: 0.5303 time to fit residues: 285.5110 Evaluate side-chains 439 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 340 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 432 GLN Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 412 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 37 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 196 optimal weight: 7.9990 chunk 277 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN B 616 ASN M 69 ASN M 79 GLN C 280 ASN N 38 HIS Q 69 ASN R 38 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112852 restraints weight = 27963.460| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.98 r_work: 0.3178 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25938 Z= 0.154 Angle : 0.643 8.811 35418 Z= 0.307 Chirality : 0.044 0.233 4224 Planarity : 0.004 0.048 4314 Dihedral : 8.639 68.706 5421 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.97 % Allowed : 22.73 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3015 helix: 0.91 (0.26), residues: 420 sheet: -0.40 (0.16), residues: 933 loop : -0.71 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 94 TYR 0.029 0.001 TYR M 49 PHE 0.025 0.002 PHE G 67 TRP 0.013 0.001 TRP F 610 HIS 0.003 0.001 HIS E 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (25788) covalent geometry : angle 0.59174 / 0.30 (35013) SS BOND : bond 0.00442 / 0.31 ( 45) SS BOND : angle 1.61511 / 1.11 ( 90) hydrogen bonds : bond 0.03743 / 2.54 ( 687) hydrogen bonds : angle 4.91250 / 3.34 ( 1827) link_ALPHA1-2 : bond 0.00268 / 0.14 ( 12) link_ALPHA1-2 : angle 2.18757 / 1.39 ( 36) link_ALPHA1-3 : bond 0.00948 / 0.56 ( 9) link_ALPHA1-3 : angle 1.43429 / 0.84 ( 27) link_ALPHA1-6 : bond 0.00259 / 0.14 ( 9) link_ALPHA1-6 : angle 1.54184 / 0.96 ( 27) link_BETA1-4 : bond 0.00457 / 0.22 ( 24) link_BETA1-4 : angle 2.15130 / 1.48 ( 72) link_NAG-ASN : bond 0.00400 / 0.29 ( 51) link_NAG-ASN : angle 3.13879 / 2.07 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 345 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7270 (mm110) cc_final: 0.6912 (mp10) REVERT: I 14 SER cc_start: 0.6124 (OUTLIER) cc_final: 0.5777 (m) REVERT: I 31 ASN cc_start: 0.8405 (m-40) cc_final: 0.8184 (m110) REVERT: I 45 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7404 (ttpt) REVERT: I 53 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7915 (mm110) REVERT: I 88 CYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7439 (p) REVERT: A 117 LYS cc_start: 0.8446 (mttt) cc_final: 0.8199 (mttt) REVERT: A 232 LYS cc_start: 0.8599 (mtpp) cc_final: 0.7749 (mmtm) REVERT: A 308 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: B 633 LYS cc_start: 0.8101 (mttt) cc_final: 0.7566 (mtmp) REVERT: L 53 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7553 (mp10) REVERT: L 63 SER cc_start: 0.8057 (t) cc_final: 0.7539 (p) REVERT: L 67 SER cc_start: 0.7732 (OUTLIER) cc_final: 0.7520 (p) REVERT: J 32 PHE cc_start: 0.8615 (m-80) cc_final: 0.8327 (m-10) REVERT: J 105 GLN cc_start: 0.7410 (mm-40) cc_final: 0.7123 (mp-120) REVERT: M 47 MET cc_start: 0.8375 (mmm) cc_final: 0.7909 (mmm) REVERT: M 53 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7865 (mm-40) REVERT: C 82 GLN cc_start: 0.7504 (mm110) cc_final: 0.7091 (tp-100) REVERT: C 95 MET cc_start: 0.9107 (ptm) cc_final: 0.8859 (ptm) REVERT: C 114 GLN cc_start: 0.7988 (mt0) cc_final: 0.7167 (mm-40) REVERT: C 117 LYS cc_start: 0.8461 (mttt) cc_final: 0.8010 (mmpt) REVERT: C 169 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7403 (mmtm) REVERT: C 232 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8283 (mtmt) REVERT: C 396 ILE cc_start: 0.7259 (pt) cc_final: 0.6914 (mm) REVERT: D 535 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (mmt) REVERT: D 588 ARG cc_start: 0.8572 (mtm110) cc_final: 0.8217 (mtm110) REVERT: D 633 LYS cc_start: 0.8111 (mttt) cc_final: 0.7624 (mtpt) REVERT: D 652 GLN cc_start: 0.8693 (mt0) cc_final: 0.8479 (mt0) REVERT: K 71 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7323 (pttm) REVERT: K 77 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: N 52 ASN cc_start: 0.7374 (OUTLIER) cc_final: 0.7119 (p0) REVERT: N 63 SER cc_start: 0.8218 (t) cc_final: 0.7778 (p) REVERT: O 21 SER cc_start: 0.7628 (m) cc_final: 0.7239 (t) REVERT: O 34 MET cc_start: 0.8872 (mmm) cc_final: 0.8451 (mmt) REVERT: O 105 GLN cc_start: 0.7258 (mm110) cc_final: 0.7046 (mp-120) REVERT: Q 14 SER cc_start: 0.6334 (OUTLIER) cc_final: 0.5896 (m) REVERT: Q 47 MET cc_start: 0.8493 (mmp) cc_final: 0.8149 (mmm) REVERT: Q 53 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8003 (mm-40) REVERT: Q 95 GLN cc_start: 0.7704 (mp-120) cc_final: 0.7438 (mm110) REVERT: E 106 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6939 (mm-30) REVERT: E 114 GLN cc_start: 0.7777 (mt0) cc_final: 0.7148 (mm-40) REVERT: E 169 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7463 (mptt) REVERT: E 232 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8306 (mtpp) REVERT: E 322 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8191 (t70) REVERT: E 504 ARG cc_start: 0.6978 (tpp-160) cc_final: 0.6531 (tpm170) REVERT: F 535 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8622 (mtp) REVERT: F 633 LYS cc_start: 0.8136 (mttt) cc_final: 0.7570 (mtpt) REVERT: F 659 ASP cc_start: 0.8731 (m-30) cc_final: 0.8453 (m-30) REVERT: P 66 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.5885 (mtm-85) REVERT: R 52 ASN cc_start: 0.7463 (p0) cc_final: 0.7212 (p0) REVERT: R 53 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7285 (mt0) REVERT: R 63 SER cc_start: 0.7891 (t) cc_final: 0.7592 (m) outliers start: 106 outliers final: 60 residues processed: 421 average time/residue: 0.5409 time to fit residues: 268.0312 Evaluate side-chains 405 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 333 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 182 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 616 ASN C 98 ASN C 280 ASN Q 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112585 restraints weight = 28144.020| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.98 r_work: 0.3174 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25938 Z= 0.161 Angle : 0.641 9.247 35418 Z= 0.307 Chirality : 0.044 0.239 4224 Planarity : 0.004 0.047 4314 Dihedral : 8.264 65.864 5421 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.76 % Allowed : 22.10 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3015 helix: 1.06 (0.26), residues: 420 sheet: -0.29 (0.16), residues: 933 loop : -0.63 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 94 TYR 0.024 0.001 TYR I 49 PHE 0.029 0.002 PHE K 57 TRP 0.011 0.002 TRP F 610 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (25788) covalent geometry : angle 0.59012 / 0.29 (35013) SS BOND : bond 0.00441 / 0.31 ( 45) SS BOND : angle 1.68540 / 1.18 ( 90) hydrogen bonds : bond 0.03758 / 2.55 ( 687) hydrogen bonds : angle 4.80280 / 3.27 ( 1827) link_ALPHA1-2 : bond 0.00269 / 0.14 ( 12) link_ALPHA1-2 : angle 2.19911 / 1.39 ( 36) link_ALPHA1-3 : bond 0.00893 / 0.53 ( 9) link_ALPHA1-3 : angle 1.45829 / 0.85 ( 27) link_ALPHA1-6 : bond 0.00241 / 0.13 ( 9) link_ALPHA1-6 : angle 1.50994 / 0.95 ( 27) link_BETA1-4 : bond 0.00433 / 0.21 ( 24) link_BETA1-4 : angle 2.11685 / 1.44 ( 72) link_NAG-ASN : bond 0.00408 / 0.29 ( 51) link_NAG-ASN : angle 3.09978 / 2.04 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 341 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7247 (mm110) cc_final: 0.6850 (mp10) REVERT: I 14 SER cc_start: 0.6080 (OUTLIER) cc_final: 0.5754 (m) REVERT: I 53 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7976 (mm-40) REVERT: I 88 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7262 (p) REVERT: A 117 LYS cc_start: 0.8412 (mttt) cc_final: 0.8158 (mttt) REVERT: A 232 LYS cc_start: 0.8597 (mtpp) cc_final: 0.7694 (mmtm) REVERT: A 308 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8165 (mtp180) REVERT: B 633 LYS cc_start: 0.8115 (mttt) cc_final: 0.7580 (mtmp) REVERT: H 77 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: L 53 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7472 (mp10) REVERT: L 63 SER cc_start: 0.8061 (t) cc_final: 0.7540 (p) REVERT: L 67 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7561 (p) REVERT: J 105 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7128 (mp-120) REVERT: M 45 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7824 (ttpt) REVERT: C 82 GLN cc_start: 0.7543 (mm110) cc_final: 0.7129 (tp-100) REVERT: C 95 MET cc_start: 0.9134 (ptm) cc_final: 0.8893 (ptm) REVERT: C 114 GLN cc_start: 0.7966 (mt0) cc_final: 0.7144 (mm-40) REVERT: C 117 LYS cc_start: 0.8420 (mttt) cc_final: 0.8003 (mmpt) REVERT: C 169 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7420 (mmtm) REVERT: C 232 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8272 (mtmt) REVERT: C 396 ILE cc_start: 0.7176 (pt) cc_final: 0.6828 (mm) REVERT: D 535 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8544 (mmt) REVERT: D 633 LYS cc_start: 0.8122 (mttt) cc_final: 0.7632 (mtpt) REVERT: K 71 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7355 (pttm) REVERT: K 77 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: N 63 SER cc_start: 0.8235 (t) cc_final: 0.7792 (p) REVERT: O 21 SER cc_start: 0.7515 (m) cc_final: 0.7138 (t) REVERT: O 34 MET cc_start: 0.8866 (mmm) cc_final: 0.8460 (mmt) REVERT: O 105 GLN cc_start: 0.7238 (mm110) cc_final: 0.7035 (mp-120) REVERT: Q 14 SER cc_start: 0.6288 (OUTLIER) cc_final: 0.5859 (m) REVERT: Q 47 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8113 (mmm) REVERT: Q 53 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8009 (mm-40) REVERT: Q 95 GLN cc_start: 0.7715 (mp-120) cc_final: 0.7445 (mm110) REVERT: E 106 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6925 (mm-30) REVERT: E 114 GLN cc_start: 0.7818 (mt0) cc_final: 0.7167 (mm-40) REVERT: E 169 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7456 (mptt) REVERT: E 232 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8376 (mtpp) REVERT: E 271 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8828 (mt) REVERT: E 322 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8341 (t70) REVERT: E 504 ARG cc_start: 0.6998 (tpp-160) cc_final: 0.6548 (tpm170) REVERT: F 535 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (mtp) REVERT: F 633 LYS cc_start: 0.8151 (mttt) cc_final: 0.7566 (mtpt) REVERT: P 66 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.5852 (mtm-85) REVERT: P 77 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: R 52 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7141 (p0) REVERT: R 53 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7245 (mt0) REVERT: R 63 SER cc_start: 0.7901 (t) cc_final: 0.7602 (m) outliers start: 127 outliers final: 83 residues processed: 434 average time/residue: 0.5775 time to fit residues: 295.3569 Evaluate side-chains 433 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 334 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 71 LYS Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 27 ILE Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 52 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 230 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 199 optimal weight: 0.3980 chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 296 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN B 616 ASN M 53 GLN M 69 ASN C 98 ASN N 53 GLN Q 31 ASN Q 69 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114359 restraints weight = 28145.452| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.97 r_work: 0.3197 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25938 Z= 0.124 Angle : 0.605 9.337 35418 Z= 0.291 Chirality : 0.043 0.231 4224 Planarity : 0.004 0.047 4314 Dihedral : 7.789 61.725 5421 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.93 % Allowed : 23.15 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3015 helix: 1.32 (0.26), residues: 420 sheet: -0.20 (0.16), residues: 939 loop : -0.52 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 94 TYR 0.026 0.001 TYR Q 49 PHE 0.029 0.001 PHE G 67 TRP 0.010 0.001 TRP F 610 HIS 0.004 0.000 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (25788) covalent geometry : angle 0.56048 / 0.28 (35013) SS BOND : bond 0.00346 / 0.24 ( 45) SS BOND : angle 1.58059 / 1.07 ( 90) hydrogen bonds : bond 0.03415 / 2.32 ( 687) hydrogen bonds : angle 4.66112 / 3.18 ( 1827) link_ALPHA1-2 : bond 0.00203 / 0.12 ( 12) link_ALPHA1-2 : angle 2.10417 / 1.33 ( 36) link_ALPHA1-3 : bond 0.01028 / 0.60 ( 9) link_ALPHA1-3 : angle 1.39853 / 0.83 ( 27) link_ALPHA1-6 : bond 0.00347 / 0.20 ( 9) link_ALPHA1-6 : angle 1.44667 / 0.91 ( 27) link_BETA1-4 : bond 0.00424 / 0.20 ( 24) link_BETA1-4 : angle 1.94142 / 1.33 ( 72) link_NAG-ASN : bond 0.00309 / 0.22 ( 51) link_NAG-ASN : angle 2.80015 / 1.86 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 339 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7232 (mm110) cc_final: 0.6839 (mp10) REVERT: I 14 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5693 (m) REVERT: I 53 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7977 (mm-40) REVERT: I 88 CYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7212 (p) REVERT: A 117 LYS cc_start: 0.8288 (mttt) cc_final: 0.8035 (mttt) REVERT: A 232 LYS cc_start: 0.8630 (mtpp) cc_final: 0.7730 (mmtm) REVERT: B 633 LYS cc_start: 0.8100 (mttt) cc_final: 0.7561 (mtmp) REVERT: H 77 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: L 53 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7434 (mp10) REVERT: L 63 SER cc_start: 0.8052 (t) cc_final: 0.7530 (p) REVERT: L 67 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7547 (p) REVERT: J 105 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7091 (mp-120) REVERT: M 79 GLN cc_start: 0.7104 (mt0) cc_final: 0.6412 (mm110) REVERT: C 82 GLN cc_start: 0.7514 (mm110) cc_final: 0.7105 (tp-100) REVERT: C 95 MET cc_start: 0.9132 (ptm) cc_final: 0.8886 (ptm) REVERT: C 114 GLN cc_start: 0.7959 (mt0) cc_final: 0.7110 (mm-40) REVERT: C 117 LYS cc_start: 0.8397 (mttt) cc_final: 0.7971 (mmpt) REVERT: C 169 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7419 (mmtm) REVERT: C 232 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8239 (mtmt) REVERT: D 535 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8519 (mmt) REVERT: D 588 ARG cc_start: 0.8545 (mtm110) cc_final: 0.8194 (mtt90) REVERT: D 633 LYS cc_start: 0.8110 (mttt) cc_final: 0.7626 (mtpt) REVERT: K 71 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7218 (pttm) REVERT: K 77 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: N 63 SER cc_start: 0.8154 (t) cc_final: 0.7707 (p) REVERT: O 21 SER cc_start: 0.7358 (m) cc_final: 0.7062 (t) REVERT: O 34 MET cc_start: 0.8837 (mmm) cc_final: 0.8422 (mmt) REVERT: O 105 GLN cc_start: 0.7205 (mm110) cc_final: 0.6999 (mp-120) REVERT: Q 14 SER cc_start: 0.6196 (OUTLIER) cc_final: 0.5780 (m) REVERT: Q 47 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8114 (mmm) REVERT: Q 53 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7869 (mm-40) REVERT: Q 95 GLN cc_start: 0.7657 (mp-120) cc_final: 0.7382 (mm110) REVERT: E 106 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6903 (mm-30) REVERT: E 114 GLN cc_start: 0.7783 (mt0) cc_final: 0.7149 (mm-40) REVERT: E 169 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7435 (mptt) REVERT: E 232 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8341 (mtpp) REVERT: E 322 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8355 (t70) REVERT: E 504 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6491 (tpm170) REVERT: F 535 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8607 (mtp) REVERT: F 633 LYS cc_start: 0.8127 (mttt) cc_final: 0.7563 (mtpt) REVERT: P 66 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.5812 (mtm-85) REVERT: P 77 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: R 52 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6942 (p0) REVERT: R 53 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7267 (mt0) REVERT: R 63 SER cc_start: 0.7894 (t) cc_final: 0.7600 (m) outliers start: 105 outliers final: 66 residues processed: 414 average time/residue: 0.6146 time to fit residues: 297.7326 Evaluate side-chains 412 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 66 ARG Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 52 ASN Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 52 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 80 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 277 optimal weight: 0.0970 chunk 138 optimal weight: 4.9990 chunk 293 optimal weight: 0.1980 chunk 179 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN A 82 GLN B 616 ASN B 625 ASN M 53 GLN C 98 ASN C 246 GLN Q 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112383 restraints weight = 28093.761| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.98 r_work: 0.3171 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25938 Z= 0.173 Angle : 0.644 9.049 35418 Z= 0.309 Chirality : 0.044 0.238 4224 Planarity : 0.004 0.046 4314 Dihedral : 7.799 62.448 5421 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.19 % Allowed : 22.77 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3015 helix: 1.22 (0.26), residues: 420 sheet: -0.15 (0.16), residues: 954 loop : -0.53 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 94 TYR 0.027 0.001 TYR M 49 PHE 0.034 0.002 PHE G 67 TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS K 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (25788) covalent geometry : angle 0.59441 / 0.30 (35013) SS BOND : bond 0.00453 / 0.31 ( 45) SS BOND : angle 1.71786 / 1.12 ( 90) hydrogen bonds : bond 0.03787 / 2.56 ( 687) hydrogen bonds : angle 4.74162 / 3.24 ( 1827) link_ALPHA1-2 : bond 0.00280 / 0.14 ( 12) link_ALPHA1-2 : angle 2.22905 / 1.41 ( 36) link_ALPHA1-3 : bond 0.00879 / 0.52 ( 9) link_ALPHA1-3 : angle 1.51660 / 0.88 ( 27) link_ALPHA1-6 : bond 0.00246 / 0.12 ( 9) link_ALPHA1-6 : angle 1.47475 / 0.93 ( 27) link_BETA1-4 : bond 0.00437 / 0.22 ( 24) link_BETA1-4 : angle 2.07031 / 1.41 ( 72) link_NAG-ASN : bond 0.00426 / 0.31 ( 51) link_NAG-ASN : angle 3.07322 / 2.02 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 333 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 105 GLN cc_start: 0.7261 (mm110) cc_final: 0.6871 (mp10) REVERT: I 14 SER cc_start: 0.5983 (OUTLIER) cc_final: 0.5671 (m) REVERT: I 45 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7979 (ttpt) REVERT: I 53 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7963 (mm-40) REVERT: I 88 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7365 (p) REVERT: A 117 LYS cc_start: 0.8298 (mttt) cc_final: 0.8046 (mttt) REVERT: A 232 LYS cc_start: 0.8593 (mtpp) cc_final: 0.7687 (mmtm) REVERT: B 633 LYS cc_start: 0.8086 (mttt) cc_final: 0.7592 (mtmp) REVERT: H 77 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: L 53 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7465 (mp10) REVERT: L 63 SER cc_start: 0.8060 (t) cc_final: 0.7537 (p) REVERT: M 45 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7713 (tttm) REVERT: C 82 GLN cc_start: 0.7538 (mm110) cc_final: 0.7130 (tp-100) REVERT: C 95 MET cc_start: 0.9157 (ptm) cc_final: 0.8892 (ptm) REVERT: C 114 GLN cc_start: 0.7891 (mt0) cc_final: 0.7053 (mm-40) REVERT: C 117 LYS cc_start: 0.8395 (mttt) cc_final: 0.7971 (mmpt) REVERT: C 169 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7424 (mmtm) REVERT: C 232 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8271 (mtmt) REVERT: D 535 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8549 (mmt) REVERT: D 633 LYS cc_start: 0.8113 (mttt) cc_final: 0.7615 (mtpt) REVERT: K 71 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7289 (pttm) REVERT: K 77 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: N 63 SER cc_start: 0.8185 (t) cc_final: 0.7737 (p) REVERT: O 21 SER cc_start: 0.7490 (m) cc_final: 0.7145 (t) REVERT: O 34 MET cc_start: 0.8854 (mmm) cc_final: 0.8472 (mmt) REVERT: O 105 GLN cc_start: 0.7162 (mm110) cc_final: 0.6925 (mp-120) REVERT: Q 14 SER cc_start: 0.6142 (OUTLIER) cc_final: 0.5770 (m) REVERT: Q 47 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: Q 53 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7892 (mm-40) REVERT: Q 70 THR cc_start: 0.7967 (t) cc_final: 0.7756 (m) REVERT: Q 95 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7402 (mm110) REVERT: E 106 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6921 (mm-30) REVERT: E 114 GLN cc_start: 0.7786 (mt0) cc_final: 0.7141 (mm-40) REVERT: E 169 LYS cc_start: 0.7991 (mtmt) cc_final: 0.7459 (mptt) REVERT: E 232 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8344 (mtpp) REVERT: E 322 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (t70) REVERT: E 504 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6546 (tpm170) REVERT: F 535 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: F 633 LYS cc_start: 0.8167 (mttt) cc_final: 0.7604 (mtpt) REVERT: P 66 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.5841 (mtm-85) REVERT: P 77 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: R 52 ASN cc_start: 0.7295 (p0) cc_final: 0.7035 (p0) REVERT: R 53 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7234 (mt0) REVERT: R 63 SER cc_start: 0.7912 (t) cc_final: 0.7620 (m) outliers start: 112 outliers final: 81 residues processed: 416 average time/residue: 0.5844 time to fit residues: 287.1601 Evaluate side-chains 422 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 328 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 182 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 121 optimal weight: 0.0770 chunk 139 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 chunk 192 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN B 616 ASN M 31 ASN M 53 GLN K 58 HIS Q 31 ASN P 58 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.159564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115762 restraints weight = 28273.576| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.98 r_work: 0.3224 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25938 Z= 0.107 Angle : 0.577 7.814 35418 Z= 0.278 Chirality : 0.042 0.223 4224 Planarity : 0.004 0.048 4314 Dihedral : 7.223 58.765 5421 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.71 % Allowed : 23.48 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3015 helix: 1.57 (0.27), residues: 420 sheet: -0.08 (0.16), residues: 963 loop : -0.42 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 94 TYR 0.033 0.001 TYR I 49 PHE 0.036 0.001 PHE G 67 TRP 0.014 0.001 TRP B 610 HIS 0.002 0.000 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (25788) covalent geometry : angle 0.53851 / 0.27 (35013) SS BOND : bond 0.00327 / 0.23 ( 45) SS BOND : angle 1.25561 / 0.87 ( 90) hydrogen bonds : bond 0.03211 / 2.18 ( 687) hydrogen bonds : angle 4.57073 / 3.13 ( 1827) link_ALPHA1-2 : bond 0.00202 / 0.13 ( 12) link_ALPHA1-2 : angle 2.05627 / 1.30 ( 36) link_ALPHA1-3 : bond 0.01062 / 0.62 ( 9) link_ALPHA1-3 : angle 1.38302 / 0.82 ( 27) link_ALPHA1-6 : bond 0.00410 / 0.24 ( 9) link_ALPHA1-6 : angle 1.41732 / 0.89 ( 27) link_BETA1-4 : bond 0.00418 / 0.20 ( 24) link_BETA1-4 : angle 1.77689 / 1.22 ( 72) link_NAG-ASN : bond 0.00263 / 0.19 ( 51) link_NAG-ASN : angle 2.55543 / 1.71 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 342 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 SER cc_start: 0.7157 (m) cc_final: 0.6884 (t) REVERT: G 87 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7528 (m) REVERT: G 105 GLN cc_start: 0.7212 (mm110) cc_final: 0.6865 (mp10) REVERT: I 14 SER cc_start: 0.5946 (OUTLIER) cc_final: 0.5634 (m) REVERT: I 53 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7858 (mm-40) REVERT: I 88 CYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7186 (p) REVERT: A 117 LYS cc_start: 0.8322 (mttt) cc_final: 0.8081 (mttt) REVERT: A 161 MET cc_start: 0.9188 (tpp) cc_final: 0.8962 (tpp) REVERT: A 232 LYS cc_start: 0.8619 (mtpp) cc_final: 0.7744 (mmtm) REVERT: B 633 LYS cc_start: 0.8032 (mttt) cc_final: 0.7556 (mtmp) REVERT: H 77 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: L 27 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8087 (t) REVERT: L 53 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7427 (mp10) REVERT: L 63 SER cc_start: 0.8046 (t) cc_final: 0.7533 (p) REVERT: J 82 MET cc_start: 0.7873 (mpt) cc_final: 0.7646 (mtm) REVERT: C 82 GLN cc_start: 0.7463 (mm110) cc_final: 0.7060 (tp-100) REVERT: C 95 MET cc_start: 0.9118 (ptm) cc_final: 0.8879 (ptm) REVERT: C 114 GLN cc_start: 0.7924 (mt0) cc_final: 0.7085 (mm-40) REVERT: C 117 LYS cc_start: 0.8410 (mttt) cc_final: 0.7989 (mmpt) REVERT: C 169 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7433 (mmtm) REVERT: C 232 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8259 (mtmt) REVERT: D 530 MET cc_start: 0.9229 (mtp) cc_final: 0.8973 (mtm) REVERT: D 535 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8552 (mmt) REVERT: D 588 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8292 (mtm110) REVERT: D 617 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8305 (mtp180) REVERT: D 633 LYS cc_start: 0.8062 (mttt) cc_final: 0.7596 (mtpt) REVERT: D 657 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 659 ASP cc_start: 0.8485 (m-30) cc_final: 0.8272 (m-30) REVERT: K 77 GLN cc_start: 0.7613 (tt0) cc_final: 0.7258 (tm-30) REVERT: N 63 SER cc_start: 0.8156 (t) cc_final: 0.7708 (p) REVERT: O 21 SER cc_start: 0.7192 (m) cc_final: 0.6902 (t) REVERT: O 34 MET cc_start: 0.8829 (mmm) cc_final: 0.8412 (mmt) REVERT: O 105 GLN cc_start: 0.7177 (mm110) cc_final: 0.6944 (mp-120) REVERT: Q 14 SER cc_start: 0.6049 (OUTLIER) cc_final: 0.5698 (m) REVERT: Q 47 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8040 (mmm) REVERT: Q 53 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7944 (mm110) REVERT: Q 95 GLN cc_start: 0.7665 (mp-120) cc_final: 0.7333 (mm110) REVERT: E 106 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7000 (mm-30) REVERT: E 114 GLN cc_start: 0.7788 (mt0) cc_final: 0.7169 (mm-40) REVERT: E 169 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7421 (mptt) REVERT: E 271 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8799 (mt) REVERT: E 322 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (t70) REVERT: E 504 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6518 (tpm170) REVERT: F 535 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8596 (mtp) REVERT: F 633 LYS cc_start: 0.8155 (mttt) cc_final: 0.7617 (mtpt) REVERT: P 66 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.5831 (mtm-85) REVERT: P 77 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: R 27 SER cc_start: 0.8586 (OUTLIER) cc_final: 0.8372 (p) REVERT: R 52 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6915 (p0) REVERT: R 53 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7272 (mt0) REVERT: R 63 SER cc_start: 0.7886 (t) cc_final: 0.7612 (m) outliers start: 99 outliers final: 64 residues processed: 415 average time/residue: 0.5803 time to fit residues: 283.0434 Evaluate side-chains 414 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 333 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 52 ASN Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 290 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 221 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN A 98 ASN B 616 ASN M 53 GLN K 58 HIS Q 31 ASN Q 69 ASN F 543 ASN P 58 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111532 restraints weight = 28247.996| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.98 r_work: 0.3161 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25938 Z= 0.204 Angle : 0.670 9.152 35418 Z= 0.321 Chirality : 0.045 0.245 4224 Planarity : 0.004 0.048 4314 Dihedral : 7.633 61.656 5421 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.52 % Allowed : 23.63 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3015 helix: 1.21 (0.26), residues: 420 sheet: -0.04 (0.16), residues: 954 loop : -0.47 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 94 TYR 0.030 0.002 TYR I 49 PHE 0.049 0.002 PHE G 67 TRP 0.014 0.002 TRP N 35 HIS 0.003 0.001 HIS H 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (25788) covalent geometry : angle 0.61905 / 0.31 (35013) SS BOND : bond 0.00514 / 0.35 ( 45) SS BOND : angle 1.68356 / 1.13 ( 90) hydrogen bonds : bond 0.04018 / 2.71 ( 687) hydrogen bonds : angle 4.77737 / 3.26 ( 1827) link_ALPHA1-2 : bond 0.00336 / 0.16 ( 12) link_ALPHA1-2 : angle 2.30678 / 1.46 ( 36) link_ALPHA1-3 : bond 0.00798 / 0.48 ( 9) link_ALPHA1-3 : angle 1.60980 / 0.92 ( 27) link_ALPHA1-6 : bond 0.00208 / 0.10 ( 9) link_ALPHA1-6 : angle 1.48959 / 0.95 ( 27) link_BETA1-4 : bond 0.00441 / 0.22 ( 24) link_BETA1-4 : angle 2.11331 / 1.43 ( 72) link_NAG-ASN : bond 0.00501 / 0.36 ( 51) link_NAG-ASN : angle 3.21585 / 2.11 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 338 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 SER cc_start: 0.7449 (m) cc_final: 0.7220 (t) REVERT: G 87 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (m) REVERT: G 105 GLN cc_start: 0.7253 (mm110) cc_final: 0.6867 (mp10) REVERT: I 14 SER cc_start: 0.6003 (OUTLIER) cc_final: 0.5694 (m) REVERT: I 45 LYS cc_start: 0.8354 (tttp) cc_final: 0.7900 (tttm) REVERT: I 53 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7910 (mm-40) REVERT: I 88 CYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7363 (p) REVERT: A 117 LYS cc_start: 0.8327 (mttt) cc_final: 0.8070 (mttt) REVERT: A 232 LYS cc_start: 0.8600 (mtpp) cc_final: 0.7696 (mmtm) REVERT: A 308 ARG cc_start: 0.8349 (mtm180) cc_final: 0.8106 (mtp180) REVERT: B 633 LYS cc_start: 0.8120 (mttt) cc_final: 0.7621 (mtmp) REVERT: H 77 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: L 53 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7452 (mp10) REVERT: L 63 SER cc_start: 0.8075 (t) cc_final: 0.7549 (p) REVERT: M 45 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7856 (tttm) REVERT: C 82 GLN cc_start: 0.7485 (mm110) cc_final: 0.7090 (tp-100) REVERT: C 95 MET cc_start: 0.9169 (ptm) cc_final: 0.8891 (ptm) REVERT: C 114 GLN cc_start: 0.7866 (mt0) cc_final: 0.7009 (mm-40) REVERT: C 117 LYS cc_start: 0.8391 (mttt) cc_final: 0.7959 (mmpt) REVERT: C 169 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7425 (mmtm) REVERT: C 232 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8285 (mtmt) REVERT: C 396 ILE cc_start: 0.7217 (pt) cc_final: 0.6887 (mm) REVERT: D 535 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8555 (mmt) REVERT: D 588 ARG cc_start: 0.8612 (mtm110) cc_final: 0.8249 (mtt90) REVERT: D 633 LYS cc_start: 0.8114 (mttt) cc_final: 0.7622 (mtpt) REVERT: K 77 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: N 63 SER cc_start: 0.8228 (t) cc_final: 0.7751 (p) REVERT: O 21 SER cc_start: 0.7581 (m) cc_final: 0.7258 (t) REVERT: O 34 MET cc_start: 0.8875 (mmm) cc_final: 0.8501 (mmt) REVERT: O 105 GLN cc_start: 0.7173 (mm110) cc_final: 0.6941 (mp-120) REVERT: Q 14 SER cc_start: 0.6142 (OUTLIER) cc_final: 0.5765 (m) REVERT: Q 47 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: Q 53 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7981 (mm110) REVERT: Q 95 GLN cc_start: 0.7693 (mp-120) cc_final: 0.7373 (mm110) REVERT: E 106 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6915 (mm-30) REVERT: E 114 GLN cc_start: 0.7733 (mt0) cc_final: 0.7106 (mm-40) REVERT: E 169 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7476 (mptt) REVERT: E 271 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8832 (mt) REVERT: E 322 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8388 (t70) REVERT: E 504 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6508 (tpm170) REVERT: F 535 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: F 633 LYS cc_start: 0.8175 (mttt) cc_final: 0.7605 (mtpt) REVERT: P 66 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.5838 (mtm-85) REVERT: P 77 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: R 52 ASN cc_start: 0.7390 (p0) cc_final: 0.7124 (p0) REVERT: R 53 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7225 (mt0) REVERT: R 63 SER cc_start: 0.7928 (t) cc_final: 0.7641 (m) outliers start: 94 outliers final: 72 residues processed: 411 average time/residue: 0.5731 time to fit residues: 278.7099 Evaluate side-chains 421 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 334 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain Q residue 14 SER Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 22 SER Chi-restraints excluded: chain Q residue 47 MET Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 66 LYS Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 21 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 252 optimal weight: 0.0670 chunk 283 optimal weight: 0.6980 chunk 58 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 267 optimal weight: 0.0370 chunk 238 optimal weight: 3.9990 chunk 177 optimal weight: 0.0010 chunk 232 optimal weight: 0.9980 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 31 ASN B 616 ASN H 58 HIS M 31 ASN M 53 GLN C 98 ASN K 58 HIS Q 31 ASN P 58 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118016 restraints weight = 28139.166| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.97 r_work: 0.3247 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25938 Z= 0.095 Angle : 0.559 7.776 35418 Z= 0.272 Chirality : 0.042 0.205 4224 Planarity : 0.004 0.046 4314 Dihedral : 6.859 58.330 5421 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 24.72 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3015 helix: 1.65 (0.27), residues: 420 sheet: 0.05 (0.16), residues: 966 loop : -0.34 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 94 TYR 0.030 0.001 TYR Q 49 PHE 0.037 0.001 PHE G 67 TRP 0.013 0.001 TRP E 479 HIS 0.004 0.000 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (25788) covalent geometry : angle 0.52668 / 0.26 (35013) SS BOND : bond 0.00300 / 0.21 ( 45) SS BOND : angle 1.12113 / 0.80 ( 90) hydrogen bonds : bond 0.03006 / 2.05 ( 687) hydrogen bonds : angle 4.51271 / 3.11 ( 1827) link_ALPHA1-2 : bond 0.00248 / 0.17 ( 12) link_ALPHA1-2 : angle 1.96290 / 1.25 ( 36) link_ALPHA1-3 : bond 0.01147 / 0.66 ( 9) link_ALPHA1-3 : angle 1.37495 / 0.82 ( 27) link_ALPHA1-6 : bond 0.00511 / 0.31 ( 9) link_ALPHA1-6 : angle 1.44318 / 0.89 ( 27) link_BETA1-4 : bond 0.00438 / 0.22 ( 24) link_BETA1-4 : angle 1.63027 / 1.12 ( 72) link_NAG-ASN : bond 0.00242 / 0.17 ( 51) link_NAG-ASN : angle 2.29703 / 1.55 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10646.54 seconds wall clock time: 181 minutes 51.92 seconds (10911.92 seconds total)