Starting phenix.real_space_refine on Thu Mar 5 07:34:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vkn_21227/03_2026/6vkn_21227.map" } resolution = 3.7 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= 0.010 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 120 5.16 5 C 12636 2.51 5 N 3384 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20220 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "I" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.07, per 1000 atoms: 0.20 Number of scatterers: 20220 At special positions: 0 Unit cell: (126.69, 124.63, 154.5, 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 120 16.00 O 4080 8.00 N 3384 7.00 C 12636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 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=2.15 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 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=2.15 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.15 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Y 4 " - " MAN Y 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA Y 3 " - " MAN Y 6 " " BMA g 3 " - " MAN g 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " FUC S 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG a 1 " - " FUC a 3 " " NAG i 1 " - " FUC i 3 " NAG-ASN " NAG A 603 " - " ASN A 234 " " NAG A 608 " - " ASN A 392 " " NAG A 611 " - " ASN A 339 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 295 " " NAG A 614 " - " ASN A 448 " " NAG A 621 " - " ASN A 301 " " NAG A 624 " - " ASN A 160 " " NAG A 625 " - " ASN A 197 " " NAG A 626 " - " ASN A 133 " " NAG A 627 " - " ASN A 355 " " NAG A 628 " - " ASN A 289 " " NAG B 704 " - " ASN B 618 " " NAG C 603 " - " ASN C 234 " " NAG C 608 " - " ASN C 392 " " NAG C 611 " - " ASN C 339 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 295 " " NAG C 614 " - " ASN C 448 " " NAG C 621 " - " ASN C 301 " " NAG C 624 " - " ASN C 160 " " NAG C 625 " - " ASN C 197 " " NAG C 626 " - " ASN C 133 " " NAG C 627 " - " ASN C 355 " " NAG C 628 " - " ASN C 289 " " NAG D 603 " - " ASN D 234 " " NAG D 608 " - " ASN D 392 " " NAG D 611 " - " ASN D 339 " " NAG D 612 " - " ASN D 332 " " NAG D 613 " - " ASN D 295 " " NAG D 614 " - " ASN D 448 " " NAG D 621 " - " ASN D 301 " " NAG D 624 " - " ASN D 160 " " NAG D 625 " - " ASN D 197 " " NAG D 626 " - " ASN D 133 " " NAG D 627 " - " ASN D 355 " " NAG D 628 " - " ASN D 289 " " NAG E 704 " - " ASN E 618 " " NAG F 704 " - " ASN F 618 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN B 611 " " NAG T 1 " - " ASN B 637 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 241 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN E 611 " " NAG b 1 " - " ASN E 637 " " NAG c 1 " - " ASN D 88 " " NAG d 1 " - " ASN D 241 " " NAG e 1 " - " ASN D 276 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 262 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN F 611 " " NAG j 1 " - " ASN F 637 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 623.3 milliseconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 22.6% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.102A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 351 removed outlier: 5.332A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.101A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 334 through 351 removed outlier: 5.331A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.101A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 334 through 351 removed outlier: 5.331A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 656 Processing helix chain 'F' and resid 657 through 659 No H-bonds generated for 'chain 'F' and resid 657 through 659' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.548A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.614A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.547A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.614A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP G 35 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD6, first strand: chain 'D' and resid 494 through 497 Processing sheet with id=AD7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 271 through 274 removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.615A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 903 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3327 1.31 - 1.44: 5476 1.44 - 1.56: 11597 1.56 - 1.69: 69 1.69 - 1.82: 153 Bond restraints: 20622 Sorted by residual: bond pdb=" NE1 TRP F 623 " pdb=" CE2 TRP F 623 " ideal model delta sigma weight residual 1.370 1.317 0.053 1.10e-02 8.26e+03 2.32e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.317 0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE1 TRP E 623 " pdb=" CE2 TRP E 623 " ideal model delta sigma weight residual 1.370 1.318 0.052 1.10e-02 8.26e+03 2.26e+01 bond pdb=" CB TYR A 484 " pdb=" CG TYR A 484 " ideal model delta sigma weight residual 1.512 1.414 0.098 2.20e-02 2.07e+03 2.00e+01 bond pdb=" CB TYR C 484 " pdb=" CG TYR C 484 " ideal model delta sigma weight residual 1.512 1.414 0.098 2.20e-02 2.07e+03 2.00e+01 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 24716 2.64 - 5.28: 2884 5.28 - 7.93: 381 7.93 - 10.57: 27 10.57 - 13.21: 3 Bond angle restraints: 28011 Sorted by residual: angle pdb=" N VAL F 570 " pdb=" CA VAL F 570 " pdb=" C VAL F 570 " ideal model delta sigma weight residual 112.12 101.76 10.36 8.40e-01 1.42e+00 1.52e+02 angle pdb=" N VAL B 570 " pdb=" CA VAL B 570 " pdb=" C VAL B 570 " ideal model delta sigma weight residual 112.12 101.78 10.34 8.40e-01 1.42e+00 1.52e+02 angle pdb=" N VAL E 570 " pdb=" CA VAL E 570 " pdb=" C VAL E 570 " ideal model delta sigma weight residual 112.12 101.80 10.32 8.40e-01 1.42e+00 1.51e+02 angle pdb=" N TRP D 35 " pdb=" CA TRP D 35 " pdb=" C TRP D 35 " ideal model delta sigma weight residual 109.54 122.75 -13.21 1.37e+00 5.33e-01 9.30e+01 angle pdb=" N TRP A 35 " pdb=" CA TRP A 35 " pdb=" C TRP A 35 " ideal model delta sigma weight residual 109.54 122.75 -13.21 1.37e+00 5.33e-01 9.30e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 13140 22.01 - 44.02: 342 44.02 - 66.04: 117 66.04 - 88.05: 36 88.05 - 110.06: 15 Dihedral angle restraints: 13650 sinusoidal: 6759 harmonic: 6891 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.47 -59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.45 -59.45 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.45 -59.45 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 13647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2661 0.111 - 0.223: 700 0.223 - 0.334: 77 0.334 - 0.445: 0 0.445 - 0.556: 3 Chirality restraints: 3441 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.15e+01 chirality pdb=" C1 BMA g 3 " pdb=" O4 NAG g 2 " pdb=" C2 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.13e+01 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.12e+01 ... (remaining 3438 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " -0.089 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN C 133 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG C 626 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " 0.089 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN A 133 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " -0.144 2.00e-02 2.50e+03 pdb=" C1 NAG A 626 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 133 " -0.089 2.00e-02 2.50e+03 9.23e-02 1.07e+02 pdb=" CG ASN D 133 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN D 133 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN D 133 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG D 626 " -0.110 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5168 2.80 - 3.32: 17101 3.32 - 3.85: 33162 3.85 - 4.37: 38123 4.37 - 4.90: 64124 Nonbonded interactions: 157678 Sorted by model distance: nonbonded pdb=" O GLY F 521 " pdb=" N LEU F 523 " model vdw 2.274 3.120 nonbonded pdb=" O GLY E 521 " pdb=" N LEU E 523 " model vdw 2.274 3.120 nonbonded pdb=" O GLY B 521 " pdb=" N LEU B 523 " model vdw 2.274 3.120 nonbonded pdb=" N ASP J 60 " pdb=" OD1 ASP J 60 " model vdw 2.414 3.120 nonbonded pdb=" N ASP L 60 " pdb=" OD1 ASP L 60 " model vdw 2.415 3.120 ... (remaining 157673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.019 0.130 20760 Z= 0.989 Angle : 1.788 13.211 28389 Z= 1.131 Chirality : 0.096 0.556 3441 Planarity : 0.009 0.070 3429 Dihedral : 12.054 110.059 9090 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.58 % Favored : 95.65 % Rotamer: Outliers : 0.85 % Allowed : 1.14 % Favored : 98.01 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2346 helix: -0.49 (0.25), residues: 375 sheet: 1.03 (0.18), residues: 702 loop : 0.84 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 429 TYR 0.060 0.008 TYR H 91 PHE 0.035 0.006 PHE A 383 TRP 0.041 0.008 TRP D 96 HIS 0.007 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.01878 (20622) covalent geometry : angle 1.76932 (28011) SS BOND : bond 0.03412 ( 36) SS BOND : angle 2.40661 ( 72) hydrogen bonds : bond 0.17981 ( 783) hydrogen bonds : angle 7.78772 ( 2241) link_ALPHA1-2 : bond 0.04581 ( 3) link_ALPHA1-2 : angle 2.96952 ( 9) link_ALPHA1-3 : bond 0.03461 ( 3) link_ALPHA1-3 : angle 2.55630 ( 9) link_ALPHA1-6 : bond 0.03629 ( 3) link_ALPHA1-6 : angle 3.03145 ( 9) link_BETA1-4 : bond 0.02577 ( 27) link_BETA1-4 : angle 3.51402 ( 81) link_BETA1-6 : bond 0.02883 ( 3) link_BETA1-6 : angle 3.67515 ( 9) link_NAG-ASN : bond 0.03011 ( 63) link_NAG-ASN : angle 2.66238 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 588 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8017 (mmm) cc_final: 0.7528 (mmt) REVERT: B 607 ASN cc_start: 0.8489 (m-40) cc_final: 0.8063 (t0) REVERT: B 652 GLN cc_start: 0.8346 (tp40) cc_final: 0.8080 (tp40) REVERT: L 100 GLN cc_start: 0.7080 (pm20) cc_final: 0.6105 (mp10) REVERT: H 5 VAL cc_start: 0.7430 (t) cc_final: 0.7221 (m) REVERT: C 150 MET cc_start: 0.7918 (mmm) cc_final: 0.7499 (mmt) REVERT: C 309 ILE cc_start: 0.9000 (tt) cc_final: 0.8713 (tt) REVERT: C 360 ARG cc_start: 0.8245 (ttm170) cc_final: 0.8021 (ttp80) REVERT: E 562 GLN cc_start: 0.6152 (mt0) cc_final: 0.5767 (tt0) REVERT: E 652 GLN cc_start: 0.8263 (tp40) cc_final: 0.7823 (tp40) REVERT: J 36 TYR cc_start: 0.9067 (m-80) cc_final: 0.8752 (m-80) REVERT: J 100 GLN cc_start: 0.7352 (pm20) cc_final: 0.6180 (mp10) REVERT: D 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7506 (mmt) REVERT: D 474 ASP cc_start: 0.6025 (t0) cc_final: 0.5820 (t0) REVERT: F 607 ASN cc_start: 0.8489 (m-40) cc_final: 0.8282 (t0) REVERT: F 635 ILE cc_start: 0.9332 (mm) cc_final: 0.9047 (tt) REVERT: F 652 GLN cc_start: 0.8423 (tp40) cc_final: 0.8089 (tp40) REVERT: K 72 THR cc_start: 0.8599 (m) cc_final: 0.8355 (p) REVERT: K 100 GLN cc_start: 0.7291 (pm20) cc_final: 0.6265 (mp10) REVERT: I 5 VAL cc_start: 0.7500 (t) cc_final: 0.7278 (m) outliers start: 18 outliers final: 1 residues processed: 597 average time/residue: 0.1761 time to fit residues: 154.3957 Evaluate side-chains 300 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 478 ASN B 543 ASN L 92 ASN C 130 GLN E 607 ASN E 658 GLN J 38 GLN J 92 ASN D 130 GLN D 478 ASN F 543 ASN K 38 GLN K 92 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109918 restraints weight = 30840.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112865 restraints weight = 20900.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114857 restraints weight = 16290.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116049 restraints weight = 13781.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116909 restraints weight = 12379.450| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20760 Z= 0.193 Angle : 0.804 12.038 28389 Z= 0.411 Chirality : 0.047 0.216 3441 Planarity : 0.004 0.034 3429 Dihedral : 7.911 58.779 4667 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 8.11 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 2346 helix: 0.47 (0.28), residues: 393 sheet: 0.77 (0.18), residues: 816 loop : 0.49 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 419 TYR 0.015 0.002 TYR A 484 PHE 0.017 0.002 PHE G 100C TRP 0.018 0.002 TRP I 103 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00421 (20622) covalent geometry : angle 0.75760 (28011) SS BOND : bond 0.00536 ( 36) SS BOND : angle 1.74775 ( 72) hydrogen bonds : bond 0.06329 ( 783) hydrogen bonds : angle 5.75338 ( 2241) link_ALPHA1-2 : bond 0.00758 ( 3) link_ALPHA1-2 : angle 1.65251 ( 9) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.89858 ( 9) link_ALPHA1-6 : bond 0.01309 ( 3) link_ALPHA1-6 : angle 1.02785 ( 9) link_BETA1-4 : bond 0.00645 ( 27) link_BETA1-4 : angle 1.89953 ( 81) link_BETA1-6 : bond 0.01455 ( 3) link_BETA1-6 : angle 2.14609 ( 9) link_NAG-ASN : bond 0.00392 ( 63) link_NAG-ASN : angle 2.96510 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7683 (mmm) cc_final: 0.6984 (mmt) REVERT: A 194 ILE cc_start: 0.9396 (tp) cc_final: 0.9134 (tt) REVERT: A 426 MET cc_start: 0.5205 (tpp) cc_final: 0.4737 (mmt) REVERT: B 624 ASP cc_start: 0.8289 (m-30) cc_final: 0.8073 (m-30) REVERT: L 100 GLN cc_start: 0.7266 (pm20) cc_final: 0.6482 (mp10) REVERT: H 68 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7451 (t) REVERT: H 81 LYS cc_start: 0.7364 (mttm) cc_final: 0.7081 (mttm) REVERT: C 150 MET cc_start: 0.7582 (mmm) cc_final: 0.7314 (mmt) REVERT: C 425 ASN cc_start: 0.8288 (t0) cc_final: 0.8084 (t0) REVERT: C 426 MET cc_start: 0.5573 (tpp) cc_final: 0.5109 (mmt) REVERT: E 652 GLN cc_start: 0.7908 (tp40) cc_final: 0.7640 (tp40) REVERT: J 61 ARG cc_start: 0.7609 (mtp180) cc_final: 0.6790 (mtm110) REVERT: J 100 GLN cc_start: 0.7422 (pm20) cc_final: 0.6651 (mp10) REVERT: G 68 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7331 (t) REVERT: G 76 ASN cc_start: 0.6736 (p0) cc_final: 0.6230 (t0) REVERT: D 150 MET cc_start: 0.7751 (mmm) cc_final: 0.7277 (mmt) REVERT: D 426 MET cc_start: 0.5551 (tpp) cc_final: 0.5315 (mmt) REVERT: F 652 GLN cc_start: 0.8104 (tp40) cc_final: 0.7861 (tp40) REVERT: F 659 ASP cc_start: 0.8391 (t70) cc_final: 0.8025 (t0) REVERT: K 72 THR cc_start: 0.8407 (m) cc_final: 0.8159 (p) REVERT: K 82 ASP cc_start: 0.8354 (m-30) cc_final: 0.7593 (m-30) REVERT: K 100 GLN cc_start: 0.7431 (pm20) cc_final: 0.6764 (mp10) REVERT: K 104 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7723 (t) outliers start: 57 outliers final: 32 residues processed: 381 average time/residue: 0.1435 time to fit residues: 85.2020 Evaluate side-chains 320 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 285 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain I residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 227 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 HIS E 625 ASN D 280 ASN D 374 HIS D 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106766 restraints weight = 31004.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109490 restraints weight = 21743.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111277 restraints weight = 17228.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112415 restraints weight = 14796.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112972 restraints weight = 13404.814| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20760 Z= 0.163 Angle : 0.700 9.362 28389 Z= 0.352 Chirality : 0.045 0.216 3441 Planarity : 0.004 0.040 3429 Dihedral : 6.475 41.764 4665 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.71 % Favored : 95.91 % Rotamer: Outliers : 2.94 % Allowed : 10.62 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.18), residues: 2346 helix: 0.35 (0.28), residues: 408 sheet: 0.66 (0.17), residues: 813 loop : 0.16 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.021 0.002 TYR I 50 PHE 0.018 0.002 PHE I 78 TRP 0.011 0.001 TRP E 571 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00367 (20622) covalent geometry : angle 0.66522 (28011) SS BOND : bond 0.00404 ( 36) SS BOND : angle 1.46577 ( 72) hydrogen bonds : bond 0.04989 ( 783) hydrogen bonds : angle 5.25908 ( 2241) link_ALPHA1-2 : bond 0.00657 ( 3) link_ALPHA1-2 : angle 1.68649 ( 9) link_ALPHA1-3 : bond 0.01184 ( 3) link_ALPHA1-3 : angle 0.95971 ( 9) link_ALPHA1-6 : bond 0.00904 ( 3) link_ALPHA1-6 : angle 1.50479 ( 9) link_BETA1-4 : bond 0.00519 ( 27) link_BETA1-4 : angle 1.51962 ( 81) link_BETA1-6 : bond 0.01182 ( 3) link_BETA1-6 : angle 2.11467 ( 9) link_NAG-ASN : bond 0.00302 ( 63) link_NAG-ASN : angle 2.40344 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 321 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7690 (mmm) cc_final: 0.7416 (mmt) REVERT: A 426 MET cc_start: 0.4990 (tpp) cc_final: 0.4787 (mmt) REVERT: B 659 ASP cc_start: 0.8540 (t70) cc_final: 0.8240 (t0) REVERT: L 81 GLU cc_start: 0.7111 (mp0) cc_final: 0.5250 (tt0) REVERT: H 81 LYS cc_start: 0.8001 (mttm) cc_final: 0.7793 (mttm) REVERT: C 150 MET cc_start: 0.7661 (mmm) cc_final: 0.7442 (mmt) REVERT: C 232 LYS cc_start: 0.8203 (mttp) cc_final: 0.7400 (tmtt) REVERT: C 426 MET cc_start: 0.5625 (tpp) cc_final: 0.5349 (mmt) REVERT: C 484 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6772 (t80) REVERT: E 659 ASP cc_start: 0.8355 (t70) cc_final: 0.8082 (t0) REVERT: J 61 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7282 (mtm110) REVERT: G 68 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7178 (t) REVERT: D 150 MET cc_start: 0.7717 (mmm) cc_final: 0.7217 (mmt) REVERT: D 425 ASN cc_start: 0.8114 (t0) cc_final: 0.7909 (t0) REVERT: D 426 MET cc_start: 0.5537 (tpp) cc_final: 0.5166 (mmt) REVERT: F 659 ASP cc_start: 0.8608 (t70) cc_final: 0.8243 (t0) REVERT: K 3 ARG cc_start: 0.6211 (mmp-170) cc_final: 0.5886 (mmp-170) REVERT: K 29 VAL cc_start: 0.8468 (m) cc_final: 0.8263 (p) REVERT: K 104 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7629 (t) outliers start: 62 outliers final: 41 residues processed: 358 average time/residue: 0.1435 time to fit residues: 81.5477 Evaluate side-chains 317 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 273 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 121 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 236 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 140 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109482 restraints weight = 31106.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111576 restraints weight = 21902.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112950 restraints weight = 18371.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.114108 restraints weight = 14904.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114359 restraints weight = 14025.736| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20760 Z= 0.126 Angle : 0.640 11.039 28389 Z= 0.320 Chirality : 0.044 0.209 3441 Planarity : 0.004 0.042 3429 Dihedral : 5.679 36.835 4665 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.07 % Favored : 96.55 % Rotamer: Outliers : 2.61 % Allowed : 12.38 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2346 helix: 0.62 (0.28), residues: 408 sheet: 0.52 (0.18), residues: 816 loop : 0.04 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 66 TYR 0.018 0.001 TYR I 50 PHE 0.018 0.002 PHE D 53 TRP 0.011 0.001 TRP D 427 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00277 (20622) covalent geometry : angle 0.60925 (28011) SS BOND : bond 0.00454 ( 36) SS BOND : angle 1.19515 ( 72) hydrogen bonds : bond 0.04273 ( 783) hydrogen bonds : angle 4.99842 ( 2241) link_ALPHA1-2 : bond 0.00588 ( 3) link_ALPHA1-2 : angle 1.71922 ( 9) link_ALPHA1-3 : bond 0.01268 ( 3) link_ALPHA1-3 : angle 1.26939 ( 9) link_ALPHA1-6 : bond 0.00769 ( 3) link_ALPHA1-6 : angle 1.48810 ( 9) link_BETA1-4 : bond 0.00524 ( 27) link_BETA1-4 : angle 1.34317 ( 81) link_BETA1-6 : bond 0.01173 ( 3) link_BETA1-6 : angle 1.76240 ( 9) link_NAG-ASN : bond 0.00300 ( 63) link_NAG-ASN : angle 2.17603 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7721 (mmm) cc_final: 0.7452 (mmt) REVERT: A 426 MET cc_start: 0.4866 (tpp) cc_final: 0.4661 (mmt) REVERT: B 659 ASP cc_start: 0.8514 (t70) cc_final: 0.8255 (t0) REVERT: L 81 GLU cc_start: 0.7168 (mp0) cc_final: 0.5260 (tt0) REVERT: H 51 ILE cc_start: 0.8714 (tt) cc_final: 0.8441 (tt) REVERT: H 81 LYS cc_start: 0.7977 (mttm) cc_final: 0.7770 (mttm) REVERT: C 150 MET cc_start: 0.7671 (mmm) cc_final: 0.7463 (mmt) REVERT: C 484 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6728 (t80) REVERT: E 659 ASP cc_start: 0.8411 (t70) cc_final: 0.8164 (t0) REVERT: J 61 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7335 (mtm110) REVERT: J 104 VAL cc_start: 0.8203 (t) cc_final: 0.7998 (t) REVERT: G 51 ILE cc_start: 0.8745 (tt) cc_final: 0.8382 (tt) REVERT: G 58 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: G 68 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7445 (t) REVERT: D 100 MET cc_start: 0.8509 (mtp) cc_final: 0.8263 (mtm) REVERT: D 103 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7210 (tm130) REVERT: D 150 MET cc_start: 0.7758 (mmm) cc_final: 0.7255 (mmt) REVERT: D 217 TYR cc_start: 0.9156 (m-80) cc_final: 0.8301 (m-80) REVERT: D 425 ASN cc_start: 0.8081 (t0) cc_final: 0.7852 (t0) REVERT: D 426 MET cc_start: 0.5544 (tpp) cc_final: 0.5207 (mmt) REVERT: F 655 LYS cc_start: 0.8602 (mtpp) cc_final: 0.8297 (ttmt) REVERT: F 659 ASP cc_start: 0.8623 (t70) cc_final: 0.8285 (t0) REVERT: K 3 ARG cc_start: 0.6176 (mmp-170) cc_final: 0.5789 (mmp-170) REVERT: K 29 VAL cc_start: 0.8565 (m) cc_final: 0.8344 (p) REVERT: K 36 TYR cc_start: 0.8940 (m-80) cc_final: 0.8726 (m-80) REVERT: K 72 THR cc_start: 0.8415 (m) cc_final: 0.8095 (p) REVERT: I 51 ILE cc_start: 0.8543 (tt) cc_final: 0.8106 (tt) REVERT: I 58 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7918 (ttp80) outliers start: 55 outliers final: 33 residues processed: 346 average time/residue: 0.1487 time to fit residues: 80.8030 Evaluate side-chains 310 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 84 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 140 optimal weight: 0.2980 chunk 186 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 105 HIS B 543 ASN C 85 HIS D 85 HIS D 103 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103705 restraints weight = 31142.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105947 restraints weight = 22326.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107152 restraints weight = 18208.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108328 restraints weight = 14958.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108584 restraints weight = 14312.505| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20760 Z= 0.217 Angle : 0.710 15.701 28389 Z= 0.353 Chirality : 0.046 0.238 3441 Planarity : 0.004 0.041 3429 Dihedral : 5.771 32.926 4665 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.13 % Favored : 95.48 % Rotamer: Outliers : 3.46 % Allowed : 12.47 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 2346 helix: 0.54 (0.28), residues: 390 sheet: 0.33 (0.18), residues: 786 loop : -0.18 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 617 TYR 0.016 0.002 TYR I 50 PHE 0.023 0.002 PHE D 53 TRP 0.012 0.001 TRP C 479 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00512 (20622) covalent geometry : angle 0.67789 (28011) SS BOND : bond 0.00509 ( 36) SS BOND : angle 1.69244 ( 72) hydrogen bonds : bond 0.04902 ( 783) hydrogen bonds : angle 5.06139 ( 2241) link_ALPHA1-2 : bond 0.00598 ( 3) link_ALPHA1-2 : angle 1.68126 ( 9) link_ALPHA1-3 : bond 0.01282 ( 3) link_ALPHA1-3 : angle 1.09795 ( 9) link_ALPHA1-6 : bond 0.00585 ( 3) link_ALPHA1-6 : angle 1.50616 ( 9) link_BETA1-4 : bond 0.00473 ( 27) link_BETA1-4 : angle 1.47091 ( 81) link_BETA1-6 : bond 0.01087 ( 3) link_BETA1-6 : angle 1.86224 ( 9) link_NAG-ASN : bond 0.00346 ( 63) link_NAG-ASN : angle 2.25318 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 292 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7810 (mmm) cc_final: 0.7296 (mmt) REVERT: A 426 MET cc_start: 0.5154 (tpp) cc_final: 0.4935 (mmt) REVERT: L 42 GLN cc_start: 0.7328 (mp10) cc_final: 0.7105 (mp10) REVERT: L 61 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7389 (ptt-90) REVERT: L 81 GLU cc_start: 0.7272 (mp0) cc_final: 0.5248 (tt0) REVERT: C 150 MET cc_start: 0.7730 (mmm) cc_final: 0.7471 (mmt) REVERT: C 484 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.6789 (t80) REVERT: E 659 ASP cc_start: 0.8582 (t70) cc_final: 0.8208 (t0) REVERT: J 61 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7438 (mtm110) REVERT: G 58 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: G 68 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7596 (t) REVERT: D 100 MET cc_start: 0.8781 (mtp) cc_final: 0.8570 (mtm) REVERT: D 150 MET cc_start: 0.7832 (mmm) cc_final: 0.7493 (mmt) REVERT: D 425 ASN cc_start: 0.8115 (t0) cc_final: 0.7901 (t0) REVERT: D 426 MET cc_start: 0.5527 (tpp) cc_final: 0.5212 (mmt) REVERT: F 659 ASP cc_start: 0.8771 (t70) cc_final: 0.8365 (t0) REVERT: K 3 ARG cc_start: 0.5876 (mmp-170) cc_final: 0.5539 (mmp-170) REVERT: K 29 VAL cc_start: 0.8571 (m) cc_final: 0.8356 (p) REVERT: K 72 THR cc_start: 0.8424 (m) cc_final: 0.8115 (p) REVERT: I 58 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7928 (ttp80) outliers start: 73 outliers final: 52 residues processed: 330 average time/residue: 0.1457 time to fit residues: 74.5134 Evaluate side-chains 324 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 149 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN D 105 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104470 restraints weight = 31124.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107133 restraints weight = 21672.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108911 restraints weight = 17193.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110080 restraints weight = 14718.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110762 restraints weight = 13275.896| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20760 Z= 0.155 Angle : 0.650 17.330 28389 Z= 0.324 Chirality : 0.045 0.213 3441 Planarity : 0.004 0.042 3429 Dihedral : 5.724 50.258 4665 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.91 % Rotamer: Outliers : 2.75 % Allowed : 13.85 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2346 helix: 0.67 (0.28), residues: 393 sheet: 0.21 (0.17), residues: 804 loop : -0.21 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 66 TYR 0.018 0.001 TYR G 50 PHE 0.023 0.002 PHE D 53 TRP 0.012 0.001 TRP H 47 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00357 (20622) covalent geometry : angle 0.61987 (28011) SS BOND : bond 0.00419 ( 36) SS BOND : angle 1.40530 ( 72) hydrogen bonds : bond 0.04461 ( 783) hydrogen bonds : angle 4.89036 ( 2241) link_ALPHA1-2 : bond 0.00529 ( 3) link_ALPHA1-2 : angle 1.74517 ( 9) link_ALPHA1-3 : bond 0.01266 ( 3) link_ALPHA1-3 : angle 0.98646 ( 9) link_ALPHA1-6 : bond 0.00585 ( 3) link_ALPHA1-6 : angle 1.52071 ( 9) link_BETA1-4 : bond 0.00436 ( 27) link_BETA1-4 : angle 1.35405 ( 81) link_BETA1-6 : bond 0.01339 ( 3) link_BETA1-6 : angle 1.70645 ( 9) link_NAG-ASN : bond 0.00294 ( 63) link_NAG-ASN : angle 2.13510 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7776 (mmm) cc_final: 0.7305 (mmt) REVERT: A 426 MET cc_start: 0.5023 (tpp) cc_final: 0.4812 (mmt) REVERT: L 61 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7567 (ptt-90) REVERT: L 81 GLU cc_start: 0.7052 (mp0) cc_final: 0.5092 (tt0) REVERT: H 51 ILE cc_start: 0.8704 (tt) cc_final: 0.8354 (tt) REVERT: C 95 MET cc_start: 0.8393 (ptm) cc_final: 0.7895 (ttm) REVERT: C 150 MET cc_start: 0.7677 (mmm) cc_final: 0.7473 (mmt) REVERT: C 484 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.6832 (t80) REVERT: E 659 ASP cc_start: 0.8619 (t70) cc_final: 0.8252 (t0) REVERT: J 61 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7455 (mtm110) REVERT: G 51 ILE cc_start: 0.8695 (tt) cc_final: 0.8334 (tt) REVERT: G 58 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7911 (ttp80) REVERT: G 68 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7576 (t) REVERT: D 150 MET cc_start: 0.7807 (mmm) cc_final: 0.7508 (mmt) REVERT: D 426 MET cc_start: 0.5476 (tpp) cc_final: 0.5102 (mmt) REVERT: F 659 ASP cc_start: 0.8788 (t70) cc_final: 0.8387 (t0) REVERT: K 3 ARG cc_start: 0.5908 (mmp-170) cc_final: 0.5472 (mmp-170) REVERT: K 29 VAL cc_start: 0.8504 (m) cc_final: 0.8208 (p) REVERT: K 30 ASP cc_start: 0.8257 (t0) cc_final: 0.7995 (t0) REVERT: K 72 THR cc_start: 0.8420 (m) cc_final: 0.8086 (p) REVERT: I 51 ILE cc_start: 0.8513 (tt) cc_final: 0.8167 (tt) REVERT: I 58 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7109 (ttm110) outliers start: 58 outliers final: 43 residues processed: 308 average time/residue: 0.1488 time to fit residues: 71.2905 Evaluate side-chains 312 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 39 LYS Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 130 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104814 restraints weight = 30973.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106234 restraints weight = 22863.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107136 restraints weight = 18659.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108176 restraints weight = 16737.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108343 restraints weight = 15391.013| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20760 Z= 0.163 Angle : 0.657 17.794 28389 Z= 0.326 Chirality : 0.045 0.221 3441 Planarity : 0.004 0.041 3429 Dihedral : 5.747 59.397 4665 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.18 % Favored : 95.40 % Rotamer: Outliers : 3.37 % Allowed : 13.47 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.18), residues: 2346 helix: 0.73 (0.28), residues: 393 sheet: 0.20 (0.17), residues: 831 loop : -0.26 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.016 0.001 TYR I 50 PHE 0.022 0.002 PHE C 53 TRP 0.010 0.001 TRP F 571 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00375 (20622) covalent geometry : angle 0.62607 (28011) SS BOND : bond 0.00643 ( 36) SS BOND : angle 1.75278 ( 72) hydrogen bonds : bond 0.04458 ( 783) hydrogen bonds : angle 4.81616 ( 2241) link_ALPHA1-2 : bond 0.00535 ( 3) link_ALPHA1-2 : angle 1.68182 ( 9) link_ALPHA1-3 : bond 0.01292 ( 3) link_ALPHA1-3 : angle 0.93750 ( 9) link_ALPHA1-6 : bond 0.00638 ( 3) link_ALPHA1-6 : angle 1.56314 ( 9) link_BETA1-4 : bond 0.00419 ( 27) link_BETA1-4 : angle 1.35504 ( 81) link_BETA1-6 : bond 0.01091 ( 3) link_BETA1-6 : angle 1.69400 ( 9) link_NAG-ASN : bond 0.00293 ( 63) link_NAG-ASN : angle 2.07205 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7756 (mmm) cc_final: 0.7304 (mmt) REVERT: L 61 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7659 (ptp90) REVERT: L 81 GLU cc_start: 0.7118 (mp0) cc_final: 0.5207 (tt0) REVERT: H 51 ILE cc_start: 0.8700 (tt) cc_final: 0.8464 (tt) REVERT: C 95 MET cc_start: 0.8432 (ptm) cc_final: 0.7917 (ttm) REVERT: C 150 MET cc_start: 0.7834 (mmm) cc_final: 0.7580 (mmt) REVERT: C 484 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.6823 (t80) REVERT: E 655 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8217 (ttmt) REVERT: E 659 ASP cc_start: 0.8765 (t70) cc_final: 0.8381 (t0) REVERT: J 61 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7506 (mtm110) REVERT: G 50 TYR cc_start: 0.9108 (p90) cc_final: 0.8845 (p90) REVERT: G 51 ILE cc_start: 0.8697 (tt) cc_final: 0.8349 (tt) REVERT: G 58 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7627 (ttm170) REVERT: G 68 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7618 (t) REVERT: D 150 MET cc_start: 0.7907 (mmm) cc_final: 0.7594 (mmt) REVERT: D 426 MET cc_start: 0.5401 (tpp) cc_final: 0.5159 (mmt) REVERT: F 659 ASP cc_start: 0.8852 (t70) cc_final: 0.8389 (t0) REVERT: K 3 ARG cc_start: 0.5978 (mmp-170) cc_final: 0.5497 (mmp-170) REVERT: K 72 THR cc_start: 0.8392 (m) cc_final: 0.8069 (p) REVERT: I 51 ILE cc_start: 0.8500 (tt) cc_final: 0.8190 (tt) REVERT: I 58 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7353 (ttm170) outliers start: 71 outliers final: 53 residues processed: 325 average time/residue: 0.1376 time to fit residues: 70.8020 Evaluate side-chains 319 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 152 optimal weight: 0.0870 chunk 233 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 chunk 135 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.1478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 105 HIS C 478 ASN E 543 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105783 restraints weight = 30969.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108292 restraints weight = 22133.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109500 restraints weight = 17138.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110416 restraints weight = 15078.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110662 restraints weight = 13745.440| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20760 Z= 0.130 Angle : 0.629 16.855 28389 Z= 0.313 Chirality : 0.044 0.226 3441 Planarity : 0.004 0.041 3429 Dihedral : 5.464 51.373 4665 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.11 % Favored : 96.38 % Rotamer: Outliers : 2.56 % Allowed : 14.75 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2346 helix: 0.92 (0.29), residues: 393 sheet: 0.18 (0.17), residues: 834 loop : -0.20 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 476 TYR 0.015 0.001 TYR I 50 PHE 0.023 0.001 PHE D 53 TRP 0.021 0.001 TRP D 112 HIS 0.004 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00289 (20622) covalent geometry : angle 0.59913 (28011) SS BOND : bond 0.00417 ( 36) SS BOND : angle 1.81966 ( 72) hydrogen bonds : bond 0.04099 ( 783) hydrogen bonds : angle 4.69044 ( 2241) link_ALPHA1-2 : bond 0.00523 ( 3) link_ALPHA1-2 : angle 1.68041 ( 9) link_ALPHA1-3 : bond 0.01261 ( 3) link_ALPHA1-3 : angle 0.88379 ( 9) link_ALPHA1-6 : bond 0.00540 ( 3) link_ALPHA1-6 : angle 1.52479 ( 9) link_BETA1-4 : bond 0.00413 ( 27) link_BETA1-4 : angle 1.30933 ( 81) link_BETA1-6 : bond 0.01274 ( 3) link_BETA1-6 : angle 1.90090 ( 9) link_NAG-ASN : bond 0.00297 ( 63) link_NAG-ASN : angle 1.96636 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7729 (mmm) cc_final: 0.7197 (mmt) REVERT: B 659 ASP cc_start: 0.8628 (t70) cc_final: 0.8332 (t0) REVERT: L 61 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7682 (ptp90) REVERT: L 81 GLU cc_start: 0.7085 (mp0) cc_final: 0.5190 (tt0) REVERT: H 16 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5694 (mp0) REVERT: H 51 ILE cc_start: 0.8628 (tt) cc_final: 0.8282 (tt) REVERT: C 95 MET cc_start: 0.8396 (ptm) cc_final: 0.7930 (ttm) REVERT: C 150 MET cc_start: 0.7802 (mmm) cc_final: 0.7521 (mmt) REVERT: C 484 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6848 (t80) REVERT: E 655 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8182 (ttmt) REVERT: E 659 ASP cc_start: 0.8690 (t70) cc_final: 0.8345 (t0) REVERT: J 61 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7519 (mtm110) REVERT: G 50 TYR cc_start: 0.9051 (p90) cc_final: 0.8780 (p90) REVERT: G 51 ILE cc_start: 0.8625 (tt) cc_final: 0.8250 (tt) REVERT: G 58 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7574 (ttm170) REVERT: G 68 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7594 (t) REVERT: D 150 MET cc_start: 0.7904 (mmm) cc_final: 0.7403 (mmt) REVERT: D 217 TYR cc_start: 0.9129 (m-80) cc_final: 0.8384 (m-80) REVERT: F 659 ASP cc_start: 0.8825 (t70) cc_final: 0.8425 (t0) REVERT: K 3 ARG cc_start: 0.5965 (mmp-170) cc_final: 0.5706 (mmp-170) REVERT: K 72 THR cc_start: 0.8299 (m) cc_final: 0.7976 (p) REVERT: K 104 VAL cc_start: 0.7806 (p) cc_final: 0.7544 (t) REVERT: I 51 ILE cc_start: 0.8419 (tt) cc_final: 0.8160 (tt) REVERT: I 58 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7284 (ttm170) outliers start: 54 outliers final: 47 residues processed: 308 average time/residue: 0.1385 time to fit residues: 66.6714 Evaluate side-chains 315 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 264 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 211 optimal weight: 0.0170 chunk 111 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107807 restraints weight = 30767.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108666 restraints weight = 23362.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109427 restraints weight = 19547.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109832 restraints weight = 18289.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110316 restraints weight = 16836.986| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20760 Z= 0.120 Angle : 0.614 17.118 28389 Z= 0.306 Chirality : 0.044 0.216 3441 Planarity : 0.004 0.049 3429 Dihedral : 5.180 41.603 4665 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.62 % Favored : 95.87 % Rotamer: Outliers : 2.61 % Allowed : 15.32 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 2346 helix: 0.98 (0.29), residues: 396 sheet: 0.29 (0.17), residues: 828 loop : -0.25 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 58 TYR 0.015 0.001 TYR I 50 PHE 0.023 0.001 PHE C 53 TRP 0.032 0.001 TRP A 112 HIS 0.008 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00264 (20622) covalent geometry : angle 0.58870 (28011) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.30893 ( 72) hydrogen bonds : bond 0.03891 ( 783) hydrogen bonds : angle 4.58578 ( 2241) link_ALPHA1-2 : bond 0.00576 ( 3) link_ALPHA1-2 : angle 1.64590 ( 9) link_ALPHA1-3 : bond 0.01186 ( 3) link_ALPHA1-3 : angle 0.82628 ( 9) link_ALPHA1-6 : bond 0.00537 ( 3) link_ALPHA1-6 : angle 1.50291 ( 9) link_BETA1-4 : bond 0.00416 ( 27) link_BETA1-4 : angle 1.30382 ( 81) link_BETA1-6 : bond 0.01001 ( 3) link_BETA1-6 : angle 1.57716 ( 9) link_NAG-ASN : bond 0.00298 ( 63) link_NAG-ASN : angle 1.87401 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8612 (m100) cc_final: 0.8360 (t-100) REVERT: A 150 MET cc_start: 0.7745 (mmm) cc_final: 0.7211 (mmt) REVERT: H 51 ILE cc_start: 0.8609 (tt) cc_final: 0.8309 (tt) REVERT: C 95 MET cc_start: 0.8376 (ptm) cc_final: 0.7899 (ttm) REVERT: C 150 MET cc_start: 0.7813 (mmm) cc_final: 0.7411 (mmt) REVERT: C 484 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6878 (t80) REVERT: E 655 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8216 (ttmt) REVERT: E 659 ASP cc_start: 0.8696 (t70) cc_final: 0.8452 (t0) REVERT: J 61 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7550 (mtm110) REVERT: G 50 TYR cc_start: 0.9052 (p90) cc_final: 0.8762 (p90) REVERT: G 51 ILE cc_start: 0.8550 (tt) cc_final: 0.8242 (tt) REVERT: G 58 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7561 (ttm170) REVERT: G 68 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7607 (t) REVERT: D 150 MET cc_start: 0.7962 (mmm) cc_final: 0.7517 (mmt) REVERT: D 217 TYR cc_start: 0.9097 (m-80) cc_final: 0.8301 (m-80) REVERT: F 659 ASP cc_start: 0.8829 (t70) cc_final: 0.8438 (t0) REVERT: K 3 ARG cc_start: 0.6025 (mmp-170) cc_final: 0.5767 (mmp-170) REVERT: K 61 ARG cc_start: 0.7856 (ptt-90) cc_final: 0.7404 (ptt-90) REVERT: K 72 THR cc_start: 0.8201 (m) cc_final: 0.7870 (p) REVERT: K 82 ASP cc_start: 0.7865 (m-30) cc_final: 0.7503 (m-30) REVERT: K 104 VAL cc_start: 0.7743 (p) cc_final: 0.7482 (t) REVERT: I 16 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5652 (tp30) REVERT: I 51 ILE cc_start: 0.8384 (tt) cc_final: 0.8126 (tt) REVERT: I 58 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7283 (ttm170) outliers start: 55 outliers final: 45 residues processed: 316 average time/residue: 0.1449 time to fit residues: 71.3645 Evaluate side-chains 319 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 85 HIS D 85 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102966 restraints weight = 31190.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105611 restraints weight = 22216.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107002 restraints weight = 17127.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107731 restraints weight = 14770.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107864 restraints weight = 13678.859| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20760 Z= 0.189 Angle : 0.681 17.630 28389 Z= 0.338 Chirality : 0.046 0.229 3441 Planarity : 0.004 0.046 3429 Dihedral : 5.430 37.261 4665 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.05 % Favored : 95.44 % Rotamer: Outliers : 2.70 % Allowed : 15.08 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2346 helix: 0.68 (0.28), residues: 399 sheet: 0.22 (0.17), residues: 825 loop : -0.42 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.013 0.001 TYR H 91 PHE 0.022 0.002 PHE D 53 TRP 0.016 0.001 TRP D 112 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00447 (20622) covalent geometry : angle 0.65354 (28011) SS BOND : bond 0.00526 ( 36) SS BOND : angle 1.76510 ( 72) hydrogen bonds : bond 0.04521 ( 783) hydrogen bonds : angle 4.76506 ( 2241) link_ALPHA1-2 : bond 0.00566 ( 3) link_ALPHA1-2 : angle 1.59418 ( 9) link_ALPHA1-3 : bond 0.01178 ( 3) link_ALPHA1-3 : angle 0.76579 ( 9) link_ALPHA1-6 : bond 0.00427 ( 3) link_ALPHA1-6 : angle 1.56676 ( 9) link_BETA1-4 : bond 0.00393 ( 27) link_BETA1-4 : angle 1.39215 ( 81) link_BETA1-6 : bond 0.00759 ( 3) link_BETA1-6 : angle 1.56443 ( 9) link_NAG-ASN : bond 0.00335 ( 63) link_NAG-ASN : angle 1.96759 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 269 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7794 (mmm) cc_final: 0.7257 (mmt) REVERT: B 652 GLN cc_start: 0.8108 (tp40) cc_final: 0.7865 (tp40) REVERT: L 81 GLU cc_start: 0.6705 (mp0) cc_final: 0.4969 (tt0) REVERT: C 150 MET cc_start: 0.7837 (mmm) cc_final: 0.7377 (mmt) REVERT: E 655 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8311 (ttmt) REVERT: E 659 ASP cc_start: 0.8828 (t70) cc_final: 0.8385 (t0) REVERT: J 61 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7591 (mtm110) REVERT: G 50 TYR cc_start: 0.9124 (p90) cc_final: 0.8889 (p90) REVERT: G 51 ILE cc_start: 0.8653 (tt) cc_final: 0.8329 (tt) REVERT: G 58 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7662 (ttm170) REVERT: G 68 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7552 (t) REVERT: D 150 MET cc_start: 0.7999 (mmm) cc_final: 0.7769 (mmt) REVERT: F 659 ASP cc_start: 0.8900 (t70) cc_final: 0.8597 (t0) REVERT: K 3 ARG cc_start: 0.5986 (mmp-170) cc_final: 0.5756 (mmp-170) REVERT: K 61 ARG cc_start: 0.7954 (ptt-90) cc_final: 0.7480 (ptt-90) REVERT: I 16 GLU cc_start: 0.6503 (mt-10) cc_final: 0.5897 (tp30) REVERT: I 51 ILE cc_start: 0.8488 (tt) cc_final: 0.8222 (tt) REVERT: I 58 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7406 (ttm170) outliers start: 57 outliers final: 49 residues processed: 301 average time/residue: 0.1414 time to fit residues: 66.8407 Evaluate side-chains 312 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107036 restraints weight = 30965.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108046 restraints weight = 24651.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109366 restraints weight = 19701.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.110362 restraints weight = 17038.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110611 restraints weight = 15778.222| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20760 Z= 0.121 Angle : 0.625 17.630 28389 Z= 0.313 Chirality : 0.044 0.220 3441 Planarity : 0.004 0.046 3429 Dihedral : 5.175 36.830 4665 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.15 % Favored : 96.33 % Rotamer: Outliers : 2.42 % Allowed : 15.65 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2346 helix: 0.87 (0.28), residues: 399 sheet: 0.29 (0.17), residues: 828 loop : -0.39 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 58 TYR 0.015 0.001 TYR I 50 PHE 0.023 0.001 PHE D 53 TRP 0.016 0.001 TRP D 112 HIS 0.002 0.001 HIS F 564 Details of bonding type rmsd covalent geometry : bond 0.00269 (20622) covalent geometry : angle 0.59978 (28011) SS BOND : bond 0.00418 ( 36) SS BOND : angle 1.55961 ( 72) hydrogen bonds : bond 0.03928 ( 783) hydrogen bonds : angle 4.59072 ( 2241) link_ALPHA1-2 : bond 0.00584 ( 3) link_ALPHA1-2 : angle 1.62296 ( 9) link_ALPHA1-3 : bond 0.01188 ( 3) link_ALPHA1-3 : angle 0.80963 ( 9) link_ALPHA1-6 : bond 0.00528 ( 3) link_ALPHA1-6 : angle 1.53895 ( 9) link_BETA1-4 : bond 0.00414 ( 27) link_BETA1-4 : angle 1.32328 ( 81) link_BETA1-6 : bond 0.00757 ( 3) link_BETA1-6 : angle 1.40519 ( 9) link_NAG-ASN : bond 0.00281 ( 63) link_NAG-ASN : angle 1.84076 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.64 seconds wall clock time: 54 minutes 15.72 seconds (3255.72 seconds total)