Starting phenix.real_space_refine on Sun Sep 13 03:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vkn_21227/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.map" model { file = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vkn_21227/09_2026/6vkn_21227.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.55, per 1000 atoms: 0.23 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: 1.79 Conformation dependent library (CDL) restraints added in 806.5 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: 0.79 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: 4.09 Time building geometry restraints manager: 2.39 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 - 17.98: 11100 17.98 - 35.96: 285 35.96 - 53.94: 99 53.94 - 71.92: 51 71.92 - 89.90: 9 Dihedral angle restraints: 11544 sinusoidal: 4653 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 11541 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: 0.05 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: 2.710 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.780 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 10.910 89.900 6984 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/Z covalent geometry : bond 0.01878 / 0.98 (20622) covalent geometry : angle 1.76932 / 1.13 (28011) SS BOND : bond 0.03412 / 2.24 ( 36) SS BOND : angle 2.40661 / 1.63 ( 72) hydrogen bonds : bond 0.17981 / 11.90 ( 783) hydrogen bonds : angle 7.78772 / 5.47 ( 2241) link_ALPHA1-2 : bond 0.04581 / 2.05 ( 3) link_ALPHA1-2 : angle 2.96952 / 1.88 ( 9) link_ALPHA1-3 : bond 0.03461 / 1.54 ( 3) link_ALPHA1-3 : angle 2.55630 / 1.62 ( 9) link_ALPHA1-6 : bond 0.03629 / 1.62 ( 3) link_ALPHA1-6 : angle 3.03145 / 1.93 ( 9) link_BETA1-4 : bond 0.02577 / 1.67 ( 27) link_BETA1-4 : angle 3.51402 / 2.35 ( 81) link_BETA1-6 : bond 0.02883 / 1.28 ( 3) link_BETA1-6 : angle 3.67515 / 2.24 ( 9) link_NAG-ASN : bond 0.03011 / 1.94 ( 63) link_NAG-ASN : angle 2.66238 / 1.80 ( 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 : 0.682 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: 0.1618 time to fit residues: 143.4950 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 : 0.717 ------------------------------------------------------------------------------- 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... 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 92 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.136254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110239 restraints weight = 31009.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112454 restraints weight = 22180.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113970 restraints weight = 18335.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115013 restraints weight = 14893.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115287 restraints weight = 14194.154| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20760 Z= 0.186 Angle : 0.798 12.188 28389 Z= 0.406 Chirality : 0.047 0.213 3441 Planarity : 0.005 0.049 3429 Dihedral : 5.596 42.668 2561 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.50 % Favored : 96.29 % Rotamer: Outliers : 2.66 % Allowed : 8.11 % Favored : 89.24 % 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: 0.72 (0.18), residues: 2346 helix: 0.43 (0.28), residues: 393 sheet: 0.75 (0.18), residues: 816 loop : 0.46 (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 H 100C TRP 0.018 0.002 TRP I 103 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (20622) covalent geometry : angle 0.75452 / 0.40 (28011) SS BOND : bond 0.00566 / 0.36 ( 36) SS BOND : angle 1.57987 / 1.09 ( 72) hydrogen bonds : bond 0.06085 / 4.11 ( 783) hydrogen bonds : angle 5.72292 / 4.06 ( 2241) link_ALPHA1-2 : bond 0.01040 / 0.45 ( 3) link_ALPHA1-2 : angle 1.55221 / 0.83 ( 9) link_ALPHA1-3 : bond 0.00891 / 0.40 ( 3) link_ALPHA1-3 : angle 1.33478 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01034 / 0.46 ( 3) link_ALPHA1-6 : angle 1.30925 / 0.72 ( 9) link_BETA1-4 : bond 0.00617 / 0.45 ( 27) link_BETA1-4 : angle 1.81654 / 1.23 ( 81) link_BETA1-6 : bond 0.01336 / 0.59 ( 3) link_BETA1-6 : angle 1.91504 / 1.09 ( 9) link_NAG-ASN : bond 0.00357 / 0.23 ( 63) link_NAG-ASN : angle 2.92111 / 2.04 ( 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 413 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7680 (mmm) cc_final: 0.6980 (mmt) REVERT: A 194 ILE cc_start: 0.9378 (tp) cc_final: 0.9123 (tt) REVERT: A 426 MET cc_start: 0.5178 (tpp) cc_final: 0.4711 (mmt) REVERT: B 624 ASP cc_start: 0.8294 (m-30) cc_final: 0.8065 (m-30) REVERT: L 100 GLN cc_start: 0.7269 (pm20) cc_final: 0.6486 (mp10) REVERT: H 68 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7543 (t) REVERT: H 76 ASN cc_start: 0.6552 (p0) cc_final: 0.6203 (t0) REVERT: H 81 LYS cc_start: 0.7380 (mttm) cc_final: 0.7144 (mttm) REVERT: C 150 MET cc_start: 0.7589 (mmm) cc_final: 0.7310 (mmt) REVERT: C 425 ASN cc_start: 0.8287 (t0) cc_final: 0.8082 (t0) REVERT: C 426 MET cc_start: 0.5445 (tpp) cc_final: 0.4962 (mmt) REVERT: E 652 GLN cc_start: 0.7899 (tp40) cc_final: 0.7646 (tp40) REVERT: J 3 ARG cc_start: 0.6009 (mmp-170) cc_final: 0.5771 (mmp-170) REVERT: J 61 ARG cc_start: 0.7650 (mtp180) cc_final: 0.7117 (mtm110) REVERT: J 100 GLN cc_start: 0.7436 (pm20) cc_final: 0.6644 (mp10) REVERT: G 32 ASN cc_start: 0.7965 (m-40) cc_final: 0.7763 (m-40) REVERT: G 68 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7358 (t) REVERT: G 76 ASN cc_start: 0.6746 (p0) cc_final: 0.6232 (t0) REVERT: D 150 MET cc_start: 0.7757 (mmm) cc_final: 0.7280 (mmt) REVERT: D 478 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.7167 (t0) REVERT: F 652 GLN cc_start: 0.8092 (tp40) cc_final: 0.7855 (tp40) REVERT: F 659 ASP cc_start: 0.8406 (t70) cc_final: 0.8050 (t0) REVERT: K 61 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7236 (mtm110) REVERT: K 72 THR cc_start: 0.8398 (m) cc_final: 0.8155 (p) REVERT: K 82 ASP cc_start: 0.8350 (m-30) cc_final: 0.7704 (m-30) REVERT: K 100 GLN cc_start: 0.7440 (pm20) cc_final: 0.6769 (mp10) REVERT: K 104 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7763 (t) outliers start: 56 outliers final: 31 residues processed: 386 average time/residue: 0.1377 time to fit residues: 83.6057 Evaluate side-chains 325 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 478 ASN 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: 0.0980 chunk 227 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 120 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 625 ASN D 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106526 restraints weight = 30988.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.109565 restraints weight = 20735.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111569 restraints weight = 15966.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112867 restraints weight = 13448.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113603 restraints weight = 12013.526| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20760 Z= 0.157 Angle : 0.693 9.245 28389 Z= 0.350 Chirality : 0.044 0.202 3441 Planarity : 0.004 0.041 3429 Dihedral : 5.273 34.444 2559 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.71 % Favored : 95.91 % Rotamer: Outliers : 2.75 % Allowed : 10.67 % Favored : 86.58 % 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: 0.38 (0.28), residues: 408 sheet: 0.64 (0.17), residues: 813 loop : 0.16 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.020 0.001 TYR I 50 PHE 0.018 0.002 PHE I 78 TRP 0.014 0.001 TRP D 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (20622) covalent geometry : angle 0.65946 / 0.34 (28011) SS BOND : bond 0.00465 / 0.28 ( 36) SS BOND : angle 1.57148 / 1.01 ( 72) hydrogen bonds : bond 0.04985 / 3.38 ( 783) hydrogen bonds : angle 5.27462 / 3.74 ( 2241) link_ALPHA1-2 : bond 0.00750 / 0.33 ( 3) link_ALPHA1-2 : angle 1.44829 / 0.81 ( 9) link_ALPHA1-3 : bond 0.00915 / 0.41 ( 3) link_ALPHA1-3 : angle 1.22417 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00671 / 0.30 ( 3) link_ALPHA1-6 : angle 1.30678 / 0.71 ( 9) link_BETA1-4 : bond 0.00498 / 0.35 ( 27) link_BETA1-4 : angle 1.39395 / 0.95 ( 81) link_BETA1-6 : bond 0.01335 / 0.59 ( 3) link_BETA1-6 : angle 1.59389 / 0.93 ( 9) link_NAG-ASN : bond 0.00287 / 0.19 ( 63) link_NAG-ASN : angle 2.35338 / 1.65 ( 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 375 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7685 (mmm) cc_final: 0.7403 (mmt) REVERT: A 426 MET cc_start: 0.4983 (tpp) cc_final: 0.4778 (mmt) REVERT: B 659 ASP cc_start: 0.8502 (t70) cc_final: 0.8233 (t0) REVERT: L 81 GLU cc_start: 0.7114 (mp0) cc_final: 0.6848 (mp0) REVERT: H 68 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (t) REVERT: H 81 LYS cc_start: 0.7889 (mttm) cc_final: 0.7670 (mttm) REVERT: C 150 MET cc_start: 0.7601 (mmm) cc_final: 0.7390 (mmt) REVERT: C 232 LYS cc_start: 0.8313 (mttp) cc_final: 0.7504 (tmtt) REVERT: C 426 MET cc_start: 0.5525 (tpp) cc_final: 0.5220 (mmt) REVERT: E 659 ASP cc_start: 0.8326 (t70) cc_final: 0.8057 (t0) REVERT: J 61 ARG cc_start: 0.7638 (mtp180) cc_final: 0.7016 (mtm110) REVERT: G 32 ASN cc_start: 0.7975 (m-40) cc_final: 0.7758 (m-40) REVERT: G 68 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7143 (t) REVERT: D 150 MET cc_start: 0.7726 (mmm) cc_final: 0.7181 (mmt) REVERT: D 425 ASN cc_start: 0.8149 (t0) cc_final: 0.7942 (t0) REVERT: F 652 GLN cc_start: 0.8239 (tp40) cc_final: 0.8020 (tp40) REVERT: F 659 ASP cc_start: 0.8584 (t70) cc_final: 0.8220 (t0) REVERT: K 3 ARG cc_start: 0.6143 (mmp-170) cc_final: 0.5847 (mmp-170) REVERT: K 29 VAL cc_start: 0.8449 (m) cc_final: 0.8248 (p) REVERT: K 61 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7252 (mtm110) REVERT: K 82 ASP cc_start: 0.8122 (m-30) cc_final: 0.7734 (m-30) REVERT: K 104 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (t) outliers start: 58 outliers final: 33 residues processed: 350 average time/residue: 0.1394 time to fit residues: 77.7185 Evaluate side-chains 309 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER 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 G residue 12 VAL Chi-restraints excluded: chain G residue 21 THR 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 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 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: 0.7980 chunk 143 optimal weight: 4.9990 chunk 170 optimal weight: 0.1980 chunk 81 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109886 restraints weight = 31270.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112224 restraints weight = 21920.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113364 restraints weight = 18005.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114601 restraints weight = 14919.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114871 restraints weight = 14060.696| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20760 Z= 0.123 Angle : 0.640 10.958 28389 Z= 0.320 Chirality : 0.044 0.196 3441 Planarity : 0.004 0.042 3429 Dihedral : 5.001 29.437 2559 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.41 % Favored : 96.29 % Rotamer: Outliers : 2.32 % Allowed : 12.19 % Favored : 85.49 % 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: 0.48 (0.18), residues: 2346 helix: 0.61 (0.28), residues: 408 sheet: 0.60 (0.18), residues: 801 loop : 0.13 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 476 TYR 0.018 0.001 TYR I 50 PHE 0.018 0.002 PHE D 53 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20622) covalent geometry : angle 0.61192 / 0.31 (28011) SS BOND : bond 0.00436 / 0.26 ( 36) SS BOND : angle 1.17440 / 0.77 ( 72) hydrogen bonds : bond 0.04239 / 2.88 ( 783) hydrogen bonds : angle 4.99056 / 3.54 ( 2241) link_ALPHA1-2 : bond 0.00661 / 0.29 ( 3) link_ALPHA1-2 : angle 1.50858 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00773 / 0.34 ( 3) link_ALPHA1-3 : angle 1.23640 / 0.72 ( 9) link_ALPHA1-6 : bond 0.00601 / 0.27 ( 3) link_ALPHA1-6 : angle 1.32777 / 0.73 ( 9) link_BETA1-4 : bond 0.00467 / 0.32 ( 27) link_BETA1-4 : angle 1.21887 / 0.84 ( 81) link_BETA1-6 : bond 0.01410 / 0.63 ( 3) link_BETA1-6 : angle 1.46717 / 0.93 ( 9) link_NAG-ASN : bond 0.00294 / 0.19 ( 63) link_NAG-ASN : angle 2.11023 / 1.49 ( 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 359 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 310 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7717 (mmm) cc_final: 0.7430 (mmt) REVERT: B 659 ASP cc_start: 0.8497 (t70) cc_final: 0.8256 (t0) REVERT: H 51 ILE cc_start: 0.8750 (tt) cc_final: 0.8462 (tt) REVERT: H 81 LYS cc_start: 0.7953 (mttm) cc_final: 0.7732 (mttm) REVERT: C 150 MET cc_start: 0.7672 (mmm) cc_final: 0.7459 (mmt) REVERT: C 232 LYS cc_start: 0.8061 (mttp) cc_final: 0.7353 (tmtt) REVERT: C 478 ASN cc_start: 0.7766 (t0) cc_final: 0.7407 (t0) REVERT: C 484 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6673 (t80) REVERT: J 61 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7365 (mtm110) REVERT: J 104 VAL cc_start: 0.8214 (t) cc_final: 0.7994 (t) REVERT: G 32 ASN cc_start: 0.8007 (m-40) cc_final: 0.7724 (m-40) REVERT: G 51 ILE cc_start: 0.8730 (tt) cc_final: 0.8359 (tt) REVERT: G 58 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7633 (ttm170) REVERT: G 68 THR cc_start: 0.7707 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 150 MET cc_start: 0.7749 (mmm) cc_final: 0.7331 (mmt) REVERT: D 425 ASN cc_start: 0.8153 (t0) cc_final: 0.7931 (t0) REVERT: F 659 ASP cc_start: 0.8584 (t70) cc_final: 0.8294 (t0) REVERT: K 3 ARG cc_start: 0.6107 (mmp-170) cc_final: 0.5631 (mmp-170) REVERT: K 29 VAL cc_start: 0.8547 (m) cc_final: 0.8331 (p) REVERT: K 36 TYR cc_start: 0.8940 (m-80) cc_final: 0.8715 (m-80) REVERT: K 61 ARG cc_start: 0.7555 (mtm110) cc_final: 0.7205 (mtm110) REVERT: K 82 ASP cc_start: 0.8062 (m-30) cc_final: 0.7753 (m-30) REVERT: I 51 ILE cc_start: 0.8537 (tt) cc_final: 0.8054 (tt) REVERT: I 58 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7853 (ttp80) outliers start: 49 outliers final: 33 residues processed: 337 average time/residue: 0.1468 time to fit residues: 77.9279 Evaluate side-chains 304 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 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 261 LEU Chi-restraints excluded: chain C residue 264 SER 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 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 346 VAL 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 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: 5.9990 chunk 99 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 231 optimal weight: 0.0570 chunk 5 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 HIS B 543 ASN C 85 HIS C 103 GLN D 85 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107193 restraints weight = 31034.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109364 restraints weight = 21865.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110732 restraints weight = 18331.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112000 restraints weight = 14784.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112239 restraints weight = 13918.685| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20760 Z= 0.150 Angle : 0.647 16.466 28389 Z= 0.322 Chirality : 0.044 0.196 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.848 24.616 2559 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.91 % Rotamer: Outliers : 2.80 % Allowed : 12.33 % Favored : 84.87 % 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: 0.28 (0.18), residues: 2346 helix: 0.71 (0.28), residues: 396 sheet: 0.42 (0.17), residues: 819 loop : -0.05 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.018 0.001 TYR I 50 PHE 0.014 0.002 PHE H 78 TRP 0.010 0.001 TRP G 103 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (20622) covalent geometry : angle 0.61963 / 0.32 (28011) SS BOND : bond 0.00445 / 0.26 ( 36) SS BOND : angle 1.48578 / 1.03 ( 72) hydrogen bonds : bond 0.04329 / 2.94 ( 783) hydrogen bonds : angle 4.86159 / 3.45 ( 2241) link_ALPHA1-2 : bond 0.00714 / 0.32 ( 3) link_ALPHA1-2 : angle 1.51975 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00790 / 0.35 ( 3) link_ALPHA1-3 : angle 1.23676 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00544 / 0.24 ( 3) link_ALPHA1-6 : angle 1.30947 / 0.72 ( 9) link_BETA1-4 : bond 0.00407 / 0.27 ( 27) link_BETA1-4 : angle 1.29106 / 0.89 ( 81) link_BETA1-6 : bond 0.01255 / 0.56 ( 3) link_BETA1-6 : angle 1.56872 / 0.99 ( 9) link_NAG-ASN : bond 0.00278 / 0.18 ( 63) link_NAG-ASN : angle 2.01484 / 1.43 ( 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 354 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7714 (mmm) cc_final: 0.7235 (mmt) REVERT: B 659 ASP cc_start: 0.8574 (t70) cc_final: 0.8292 (t0) REVERT: L 61 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7461 (ptt-90) REVERT: L 81 GLU cc_start: 0.6977 (mp0) cc_final: 0.5342 (tt0) REVERT: H 101 ASP cc_start: 0.7789 (m-30) cc_final: 0.7541 (m-30) REVERT: C 150 MET cc_start: 0.7722 (mmm) cc_final: 0.7510 (mmt) REVERT: C 426 MET cc_start: 0.5626 (mmt) cc_final: 0.5409 (mmt) REVERT: C 484 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6744 (t80) REVERT: J 61 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7397 (mtm110) REVERT: J 104 VAL cc_start: 0.8161 (t) cc_final: 0.7948 (t) REVERT: G 32 ASN cc_start: 0.8107 (m-40) cc_final: 0.7813 (m-40) REVERT: G 58 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7746 (ttp-170) REVERT: D 150 MET cc_start: 0.7811 (mmm) cc_final: 0.7281 (mmt) REVERT: D 478 ASN cc_start: 0.7781 (t0) cc_final: 0.7417 (t0) REVERT: F 659 ASP cc_start: 0.8746 (t70) cc_final: 0.8373 (t0) REVERT: K 3 ARG cc_start: 0.6028 (mmp-170) cc_final: 0.5632 (mmp-170) REVERT: K 29 VAL cc_start: 0.8550 (m) cc_final: 0.8345 (p) REVERT: I 58 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7401 (ttm110) outliers start: 59 outliers final: 40 residues processed: 332 average time/residue: 0.1428 time to fit residues: 74.7240 Evaluate side-chains 311 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 346 VAL 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 L residue 106 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 H residue 107 VAL 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 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 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 103 TRP Chi-restraints excluded: chain D residue 120 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 149 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 182 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 92 ASN C 103 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.133211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.106896 restraints weight = 31025.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109660 restraints weight = 21524.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111489 restraints weight = 16898.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112672 restraints weight = 14410.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113315 restraints weight = 12975.311| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4398 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= 0.130 Angle : 0.620 14.491 28389 Z= 0.309 Chirality : 0.044 0.191 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.764 24.819 2559 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.91 % Rotamer: Outliers : 2.51 % Allowed : 13.32 % Favored : 84.16 % 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: 0.29 (0.18), residues: 2346 helix: 0.89 (0.28), residues: 396 sheet: 0.36 (0.17), residues: 834 loop : -0.07 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.021 0.001 TYR G 50 PHE 0.022 0.002 PHE C 53 TRP 0.014 0.001 TRP D 112 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20622) covalent geometry : angle 0.59474 / 0.30 (28011) SS BOND : bond 0.00628 / 0.35 ( 36) SS BOND : angle 1.23225 / 0.83 ( 72) hydrogen bonds : bond 0.04072 / 2.77 ( 783) hydrogen bonds : angle 4.74095 / 3.36 ( 2241) link_ALPHA1-2 : bond 0.00684 / 0.31 ( 3) link_ALPHA1-2 : angle 1.53886 / 0.85 ( 9) link_ALPHA1-3 : bond 0.00713 / 0.32 ( 3) link_ALPHA1-3 : angle 1.27817 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00504 / 0.22 ( 3) link_ALPHA1-6 : angle 1.31843 / 0.73 ( 9) link_BETA1-4 : bond 0.00401 / 0.27 ( 27) link_BETA1-4 : angle 1.22098 / 0.84 ( 81) link_BETA1-6 : bond 0.01142 / 0.51 ( 3) link_BETA1-6 : angle 1.63645 / 1.01 ( 9) link_NAG-ASN : bond 0.00273 / 0.17 ( 63) link_NAG-ASN : angle 1.90074 / 1.35 ( 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 341 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7703 (mmm) cc_final: 0.7236 (mmt) REVERT: B 659 ASP cc_start: 0.8645 (t70) cc_final: 0.8361 (t0) REVERT: L 61 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7606 (ptt-90) REVERT: L 81 GLU cc_start: 0.6643 (mp0) cc_final: 0.4978 (tt0) REVERT: H 51 ILE cc_start: 0.8620 (tt) cc_final: 0.8222 (tt) REVERT: C 150 MET cc_start: 0.7652 (mmm) cc_final: 0.7439 (mmt) REVERT: C 484 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6767 (t80) REVERT: E 652 GLN cc_start: 0.8076 (tp40) cc_final: 0.7850 (tp40) REVERT: J 61 ARG cc_start: 0.7838 (mtp180) cc_final: 0.7454 (mtm110) REVERT: G 32 ASN cc_start: 0.8103 (m-40) cc_final: 0.7851 (m-40) REVERT: G 51 ILE cc_start: 0.8597 (tt) cc_final: 0.8191 (tt) REVERT: G 58 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7830 (ttp80) REVERT: D 150 MET cc_start: 0.7790 (mmm) cc_final: 0.7314 (mmt) REVERT: D 217 TYR cc_start: 0.9140 (m-80) cc_final: 0.8402 (m-80) REVERT: D 478 ASN cc_start: 0.7834 (t0) cc_final: 0.7560 (t0) REVERT: F 659 ASP cc_start: 0.8770 (t70) cc_final: 0.8398 (t0) REVERT: K 3 ARG cc_start: 0.5880 (mmp-170) cc_final: 0.5438 (mmp-170) REVERT: K 72 THR cc_start: 0.8332 (m) cc_final: 0.7997 (p) REVERT: K 104 VAL cc_start: 0.7799 (p) cc_final: 0.7558 (t) REVERT: I 51 ILE cc_start: 0.8402 (tt) cc_final: 0.8080 (tt) REVERT: I 58 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7257 (ttm170) outliers start: 53 outliers final: 40 residues processed: 318 average time/residue: 0.1478 time to fit residues: 73.7621 Evaluate side-chains 308 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 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 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 115 SER 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 264 SER 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 15 SER 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 182 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 396 ILE 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 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: 0.9980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN C 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106754 restraints weight = 30835.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109530 restraints weight = 21123.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111378 restraints weight = 16524.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112437 restraints weight = 14016.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113329 restraints weight = 12644.263| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4562 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= 0.118 Angle : 0.610 15.000 28389 Z= 0.305 Chirality : 0.044 0.221 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.627 21.996 2559 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.28 % Favored : 96.21 % Rotamer: Outliers : 2.70 % Allowed : 13.61 % Favored : 83.69 % 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: 0.32 (0.18), residues: 2346 helix: 0.99 (0.28), residues: 396 sheet: 0.40 (0.17), residues: 834 loop : -0.11 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.016 0.001 TYR I 50 PHE 0.021 0.001 PHE D 53 TRP 0.022 0.001 TRP A 112 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20622) covalent geometry : angle 0.58382 / 0.30 (28011) SS BOND : bond 0.00404 / 0.25 ( 36) SS BOND : angle 1.67826 / 1.22 ( 72) hydrogen bonds : bond 0.03838 / 2.61 ( 783) hydrogen bonds : angle 4.64174 / 3.29 ( 2241) link_ALPHA1-2 : bond 0.00731 / 0.33 ( 3) link_ALPHA1-2 : angle 1.52909 / 0.85 ( 9) link_ALPHA1-3 : bond 0.00697 / 0.31 ( 3) link_ALPHA1-3 : angle 1.29288 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00486 / 0.22 ( 3) link_ALPHA1-6 : angle 1.32333 / 0.74 ( 9) link_BETA1-4 : bond 0.00391 / 0.26 ( 27) link_BETA1-4 : angle 1.20436 / 0.82 ( 81) link_BETA1-6 : bond 0.01035 / 0.47 ( 3) link_BETA1-6 : angle 1.61241 / 0.99 ( 9) link_NAG-ASN : bond 0.00269 / 0.17 ( 63) link_NAG-ASN : angle 1.82175 / 1.30 ( 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 336 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.806 Fit side-chains REVERT: A 150 MET cc_start: 0.7732 (mmm) cc_final: 0.7273 (mmt) REVERT: B 659 ASP cc_start: 0.8659 (t70) cc_final: 0.8384 (t0) REVERT: L 61 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7738 (ptt-90) REVERT: H 51 ILE cc_start: 0.8589 (tt) cc_final: 0.8207 (tt) REVERT: C 95 MET cc_start: 0.8452 (ptm) cc_final: 0.7770 (ttp) REVERT: C 150 MET cc_start: 0.7715 (mmm) cc_final: 0.7492 (mmt) REVERT: C 484 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.6698 (t80) REVERT: E 655 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8107 (ttmt) REVERT: J 3 ARG cc_start: 0.6061 (mmp-170) cc_final: 0.5831 (mmp-170) REVERT: J 61 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7427 (mtm110) REVERT: G 32 ASN cc_start: 0.8170 (m-40) cc_final: 0.7908 (m-40) REVERT: G 51 ILE cc_start: 0.8609 (tt) cc_final: 0.8250 (tt) REVERT: G 58 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7694 (ttp80) REVERT: D 150 MET cc_start: 0.7798 (mmm) cc_final: 0.7343 (mmt) REVERT: D 217 TYR cc_start: 0.9110 (m-80) cc_final: 0.8337 (m-80) REVERT: F 659 ASP cc_start: 0.8806 (t70) cc_final: 0.8383 (t0) REVERT: K 3 ARG cc_start: 0.5846 (mmp-170) cc_final: 0.5366 (mmp-170) REVERT: K 72 THR cc_start: 0.8246 (m) cc_final: 0.7915 (p) REVERT: K 81 GLU cc_start: 0.7025 (mp0) cc_final: 0.5125 (tt0) REVERT: K 104 VAL cc_start: 0.7796 (p) cc_final: 0.7536 (t) REVERT: I 51 ILE cc_start: 0.8339 (tt) cc_final: 0.8058 (tt) REVERT: I 58 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7233 (ttm170) outliers start: 57 outliers final: 46 residues processed: 311 average time/residue: 0.1427 time to fit residues: 70.4249 Evaluate side-chains 313 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 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 210 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 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 J residue 53 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 103 TRP 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 373 THR Chi-restraints excluded: chain D residue 396 ILE 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 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: 0.8980 chunk 233 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 116 optimal weight: 0.0270 chunk 135 optimal weight: 0.1980 chunk 138 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN J 92 ASN D 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108257 restraints weight = 30885.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.110600 restraints weight = 21839.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112089 restraints weight = 17552.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112951 restraints weight = 14475.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113220 restraints weight = 13766.649| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20760 Z= 0.116 Angle : 0.610 17.808 28389 Z= 0.304 Chirality : 0.043 0.219 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.532 21.966 2559 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.24 % Favored : 96.25 % Rotamer: Outliers : 2.80 % Allowed : 13.94 % Favored : 83.26 % 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: 0.35 (0.18), residues: 2346 helix: 1.06 (0.29), residues: 396 sheet: 0.43 (0.18), residues: 834 loop : -0.11 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 58 TYR 0.018 0.001 TYR G 50 PHE 0.022 0.001 PHE D 53 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (20622) covalent geometry : angle 0.58522 / 0.30 (28011) SS BOND : bond 0.00429 / 0.23 ( 36) SS BOND : angle 1.71214 / 1.27 ( 72) hydrogen bonds : bond 0.03739 / 2.55 ( 783) hydrogen bonds : angle 4.54946 / 3.22 ( 2241) link_ALPHA1-2 : bond 0.00668 / 0.30 ( 3) link_ALPHA1-2 : angle 1.50631 / 0.83 ( 9) link_ALPHA1-3 : bond 0.00681 / 0.30 ( 3) link_ALPHA1-3 : angle 1.30677 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00475 / 0.21 ( 3) link_ALPHA1-6 : angle 1.33697 / 0.75 ( 9) link_BETA1-4 : bond 0.00393 / 0.26 ( 27) link_BETA1-4 : angle 1.19631 / 0.82 ( 81) link_BETA1-6 : bond 0.00884 / 0.39 ( 3) link_BETA1-6 : angle 1.54182 / 0.93 ( 9) link_NAG-ASN : bond 0.00282 / 0.18 ( 63) link_NAG-ASN : angle 1.75585 / 1.26 ( 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 330 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.775 Fit side-chains REVERT: A 150 MET cc_start: 0.7775 (mmm) cc_final: 0.7262 (mmt) REVERT: B 659 ASP cc_start: 0.8637 (t70) cc_final: 0.8401 (t0) REVERT: L 81 GLU cc_start: 0.6245 (mp0) cc_final: 0.4622 (tt0) REVERT: H 51 ILE cc_start: 0.8563 (tt) cc_final: 0.8206 (tt) REVERT: C 95 MET cc_start: 0.8415 (ptm) cc_final: 0.7891 (ttm) REVERT: C 150 MET cc_start: 0.7766 (mmm) cc_final: 0.7477 (mmt) REVERT: C 484 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6671 (t80) REVERT: E 655 LYS cc_start: 0.8463 (mtpp) cc_final: 0.8104 (ttmt) REVERT: J 61 ARG cc_start: 0.7908 (mtp180) cc_final: 0.7500 (mtm110) REVERT: G 32 ASN cc_start: 0.8205 (m-40) cc_final: 0.7921 (m-40) REVERT: G 51 ILE cc_start: 0.8574 (tt) cc_final: 0.8232 (tt) REVERT: G 58 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7468 (ttm170) REVERT: D 150 MET cc_start: 0.7850 (mmm) cc_final: 0.7405 (mmt) REVERT: F 659 ASP cc_start: 0.8783 (t70) cc_final: 0.8446 (t0) REVERT: K 3 ARG cc_start: 0.5934 (mmp-170) cc_final: 0.5662 (mmp-170) REVERT: K 72 THR cc_start: 0.8194 (m) cc_final: 0.7863 (p) REVERT: K 104 VAL cc_start: 0.7732 (p) cc_final: 0.7484 (t) REVERT: I 51 ILE cc_start: 0.8309 (tt) cc_final: 0.8043 (tt) REVERT: I 58 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7131 (ttm170) outliers start: 59 outliers final: 49 residues processed: 305 average time/residue: 0.1440 time to fit residues: 68.7612 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 264 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 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 J residue 53 SER Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG 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 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 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER 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: 1.9990 chunk 114 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN J 92 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.132376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106438 restraints weight = 30876.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108750 restraints weight = 21986.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109978 restraints weight = 17901.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111371 restraints weight = 14986.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111494 restraints weight = 13741.346| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20760 Z= 0.144 Angle : 0.632 16.470 28389 Z= 0.315 Chirality : 0.044 0.223 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.564 22.188 2559 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.54 % Favored : 95.95 % Rotamer: Outliers : 2.80 % Allowed : 14.22 % Favored : 82.98 % 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: 0.28 (0.18), residues: 2346 helix: 0.99 (0.28), residues: 396 sheet: 0.40 (0.17), residues: 834 loop : -0.17 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 58 TYR 0.016 0.001 TYR I 50 PHE 0.022 0.002 PHE D 53 TRP 0.022 0.001 TRP A 112 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (20622) covalent geometry : angle 0.61048 / 0.31 (28011) SS BOND : bond 0.00408 / 0.25 ( 36) SS BOND : angle 1.30290 / 0.89 ( 72) hydrogen bonds : bond 0.04037 / 2.74 ( 783) hydrogen bonds : angle 4.59301 / 3.25 ( 2241) link_ALPHA1-2 : bond 0.00664 / 0.29 ( 3) link_ALPHA1-2 : angle 1.49720 / 0.82 ( 9) link_ALPHA1-3 : bond 0.00692 / 0.31 ( 3) link_ALPHA1-3 : angle 1.29822 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00460 / 0.21 ( 3) link_ALPHA1-6 : angle 1.32255 / 0.74 ( 9) link_BETA1-4 : bond 0.00381 / 0.25 ( 27) link_BETA1-4 : angle 1.26244 / 0.86 ( 81) link_BETA1-6 : bond 0.00702 / 0.32 ( 3) link_BETA1-6 : angle 1.48520 / 0.89 ( 9) link_NAG-ASN : bond 0.00281 / 0.17 ( 63) link_NAG-ASN : angle 1.75926 / 1.26 ( 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 335 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 0.760 Fit side-chains REVERT: A 150 MET cc_start: 0.7780 (mmm) cc_final: 0.7309 (mmt) REVERT: B 652 GLN cc_start: 0.8092 (tp40) cc_final: 0.7820 (tp40) REVERT: B 659 ASP cc_start: 0.8715 (t70) cc_final: 0.8442 (t0) REVERT: H 16 GLU cc_start: 0.5905 (mt-10) cc_final: 0.5653 (mt-10) REVERT: H 51 ILE cc_start: 0.8668 (tt) cc_final: 0.8297 (tt) REVERT: C 95 MET cc_start: 0.8396 (ptm) cc_final: 0.7919 (ttm) REVERT: C 150 MET cc_start: 0.7784 (mmm) cc_final: 0.7405 (mmt) REVERT: C 484 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.6656 (t80) REVERT: E 655 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8193 (ttmt) REVERT: J 61 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7531 (mtm110) REVERT: G 32 ASN cc_start: 0.8094 (m-40) cc_final: 0.7841 (m-40) REVERT: G 51 ILE cc_start: 0.8618 (tt) cc_final: 0.8286 (tt) REVERT: G 58 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: D 150 MET cc_start: 0.7876 (mmm) cc_final: 0.7453 (mmt) REVERT: D 217 TYR cc_start: 0.9047 (m-80) cc_final: 0.8282 (m-80) REVERT: F 659 ASP cc_start: 0.8843 (t70) cc_final: 0.8480 (t0) REVERT: K 3 ARG cc_start: 0.5990 (mmp-170) cc_final: 0.5742 (mmp-170) REVERT: K 61 ARG cc_start: 0.7713 (ptt-90) cc_final: 0.7236 (ptt-90) REVERT: K 72 THR cc_start: 0.8277 (m) cc_final: 0.7854 (p) REVERT: K 81 GLU cc_start: 0.6836 (mp0) cc_final: 0.4947 (tt0) REVERT: K 104 VAL cc_start: 0.7734 (p) cc_final: 0.7496 (t) REVERT: I 51 ILE cc_start: 0.8349 (tt) cc_final: 0.8077 (tt) REVERT: I 58 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7196 (ttm170) outliers start: 59 outliers final: 52 residues processed: 309 average time/residue: 0.1418 time to fit residues: 69.2190 Evaluate side-chains 322 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 264 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 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 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG 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 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 68 THR 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: 0.3980 chunk 9 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3593 r_free = 0.3593 target = 0.131072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105482 restraints weight = 31211.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107053 restraints weight = 22759.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108100 restraints weight = 18506.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109018 restraints weight = 16575.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109196 restraints weight = 15180.922| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4904 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= 0.158 Angle : 0.646 16.240 28389 Z= 0.323 Chirality : 0.045 0.248 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.655 22.309 2559 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.45 % Favored : 96.04 % Rotamer: Outliers : 2.75 % Allowed : 14.75 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 2346 helix: 0.87 (0.28), residues: 396 sheet: 0.32 (0.17), residues: 834 loop : -0.27 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.015 0.001 TYR I 50 PHE 0.022 0.002 PHE D 53 TRP 0.009 0.001 TRP F 571 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (20622) covalent geometry : angle 0.62191 / 0.32 (28011) SS BOND : bond 0.00481 / 0.27 ( 36) SS BOND : angle 1.60705 / 1.17 ( 72) hydrogen bonds : bond 0.04219 / 2.86 ( 783) hydrogen bonds : angle 4.64246 / 3.28 ( 2241) link_ALPHA1-2 : bond 0.00664 / 0.29 ( 3) link_ALPHA1-2 : angle 1.49545 / 0.82 ( 9) link_ALPHA1-3 : bond 0.00677 / 0.30 ( 3) link_ALPHA1-3 : angle 1.31405 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00428 / 0.19 ( 3) link_ALPHA1-6 : angle 1.32716 / 0.75 ( 9) link_BETA1-4 : bond 0.00377 / 0.25 ( 27) link_BETA1-4 : angle 1.29198 / 0.88 ( 81) link_BETA1-6 : bond 0.00775 / 0.34 ( 3) link_BETA1-6 : angle 1.64897 / 0.98 ( 9) link_NAG-ASN : bond 0.00286 / 0.18 ( 63) link_NAG-ASN : angle 1.78763 / 1.28 ( 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 328 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.590 Fit side-chains REVERT: A 150 MET cc_start: 0.7804 (mmm) cc_final: 0.7330 (mmt) REVERT: B 659 ASP cc_start: 0.8757 (t70) cc_final: 0.8434 (t0) REVERT: L 81 GLU cc_start: 0.6529 (mp0) cc_final: 0.4904 (tt0) REVERT: H 51 ILE cc_start: 0.8652 (tt) cc_final: 0.8297 (tt) REVERT: C 95 MET cc_start: 0.8460 (ptm) cc_final: 0.7962 (ttm) REVERT: C 150 MET cc_start: 0.7802 (mmm) cc_final: 0.7349 (mmt) REVERT: E 655 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8239 (ttmt) REVERT: J 61 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7557 (mtm110) REVERT: J 81 GLU cc_start: 0.7645 (mp0) cc_final: 0.5821 (tt0) REVERT: G 32 ASN cc_start: 0.8068 (m-40) cc_final: 0.7785 (m-40) REVERT: G 51 ILE cc_start: 0.8628 (tt) cc_final: 0.8303 (tt) REVERT: G 58 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7600 (ttm170) REVERT: D 150 MET cc_start: 0.7921 (mmm) cc_final: 0.7511 (mmt) REVERT: D 217 TYR cc_start: 0.9090 (m-80) cc_final: 0.8308 (m-80) REVERT: F 659 ASP cc_start: 0.8873 (t70) cc_final: 0.8488 (t0) REVERT: K 3 ARG cc_start: 0.5937 (mmp-170) cc_final: 0.5698 (mmp-170) REVERT: K 61 ARG cc_start: 0.7781 (ptt-90) cc_final: 0.7337 (ptt-90) REVERT: K 72 THR cc_start: 0.8255 (m) cc_final: 0.7931 (p) REVERT: K 104 VAL cc_start: 0.7735 (p) cc_final: 0.7504 (t) REVERT: I 16 GLU cc_start: 0.6357 (mt-10) cc_final: 0.5736 (tp30) REVERT: I 51 ILE cc_start: 0.8377 (tt) cc_final: 0.8155 (tt) REVERT: I 58 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7035 (ttm110) outliers start: 58 outliers final: 51 residues processed: 304 average time/residue: 0.1394 time to fit residues: 66.5475 Evaluate side-chains 317 residues out of total 2109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 371 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 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG 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 68 THR 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: 1.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3593 r_free = 0.3593 target = 0.131149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105152 restraints weight = 31046.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107309 restraints weight = 22155.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.108619 restraints weight = 18334.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109664 restraints weight = 15104.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109930 restraints weight = 14226.981| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5002 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= 0.150 Angle : 0.639 16.594 28389 Z= 0.320 Chirality : 0.044 0.255 3441 Planarity : 0.004 0.041 3429 Dihedral : 4.656 24.959 2559 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.71 % Favored : 95.78 % Rotamer: Outliers : 2.61 % Allowed : 15.03 % Favored : 82.36 % 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: 0.86 (0.28), residues: 396 sheet: 0.25 (0.18), residues: 810 loop : -0.37 (0.20), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 13 TYR 0.015 0.001 TYR I 50 PHE 0.023 0.002 PHE D 53 TRP 0.010 0.001 TRP D 427 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (20622) covalent geometry : angle 0.61589 / 0.32 (28011) SS BOND : bond 0.00424 / 0.26 ( 36) SS BOND : angle 1.57012 / 1.13 ( 72) hydrogen bonds : bond 0.04155 / 2.82 ( 783) hydrogen bonds : angle 4.62515 / 3.26 ( 2241) link_ALPHA1-2 : bond 0.00673 / 0.30 ( 3) link_ALPHA1-2 : angle 1.48432 / 0.81 ( 9) link_ALPHA1-3 : bond 0.00661 / 0.29 ( 3) link_ALPHA1-3 : angle 1.32140 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00421 / 0.19 ( 3) link_ALPHA1-6 : angle 1.33158 / 0.75 ( 9) link_BETA1-4 : bond 0.00377 / 0.25 ( 27) link_BETA1-4 : angle 1.29239 / 0.88 ( 81) link_BETA1-6 : bond 0.00660 / 0.29 ( 3) link_BETA1-6 : angle 1.53453 / 0.91 ( 9) link_NAG-ASN : bond 0.00287 / 0.17 ( 63) link_NAG-ASN : angle 1.77169 / 1.27 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3169.50 seconds wall clock time: 55 minutes 55.55 seconds (3355.55 seconds total)