Starting phenix.real_space_refine on Sun Sep 13 02:01:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo1_21257/09_2026/6vo1_21257.cif" } resolution = 3.88 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= 0.001 sd= 0.073 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 123 5.16 5 C 12396 2.51 5 N 3300 2.21 5 O 3987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 19806 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "E" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.77, per 1000 atoms: 0.24 Number of scatterers: 19806 At special positions: 0 Unit cell: (170.2, 166.75, 119.6, 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 123 16.00 O 3987 8.00 N 3300 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.15 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.04 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 A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.15 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=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.04 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 C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.15 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=2.04 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=2.02 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=2.04 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 D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA Z 3 " - " MAN Z 6 " " BMA i 3 " - " MAN i 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 618 " - " ASN A 295 " " NAG A 621 " - " ASN A 386 " " NAG A 626 " - " ASN A 355 " " NAG A 627 " - " ASN A 339 " " NAG A 628 " - " ASN A 133 " " NAG A 629 " - " ASN A 197 " " NAG C 618 " - " ASN C 295 " " NAG C 621 " - " ASN C 386 " " NAG C 626 " - " ASN C 355 " " NAG C 627 " - " ASN C 339 " " NAG C 628 " - " ASN C 133 " " NAG C 629 " - " ASN C 197 " " NAG D 618 " - " ASN D 295 " " NAG D 621 " - " ASN D 386 " " NAG D 626 " - " ASN D 355 " " NAG D 627 " - " ASN D 339 " " NAG D 628 " - " ASN D 133 " " NAG D 629 " - " ASN D 197 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN A 448 " " NAG V 1 " - " ASN C 88 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 392 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN D 88 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 160 " " NAG h 1 " - " ASN D 234 " " NAG i 1 " - " ASN D 262 " " NAG j 1 " - " ASN D 276 " " NAG k 1 " - " ASN D 332 " " NAG l 1 " - " ASN D 392 " " NAG m 1 " - " ASN D 448 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 776.6 milliseconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 22.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (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 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (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 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 560 through 565 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.581A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (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 195 through 198 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 560 through 565 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.095A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE H 48 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR H 59 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN H 50 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR H 57 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 48 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR G 59 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN G 50 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR G 57 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.073A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE I 48 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 59 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN I 50 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR I 57 " --> pdb=" O ASN I 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (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: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.588A 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 removed outlier: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 1953 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: 4.36 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4204 1.32 - 1.45: 6292 1.45 - 1.58: 9547 1.58 - 1.72: 6 1.72 - 1.85: 156 Bond restraints: 20205 Sorted by residual: bond pdb=" CB TYR J 50 " pdb=" CG TYR J 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR L 50 " pdb=" CG TYR L 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR K 50 " pdb=" CG TYR K 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.64e+01 bond pdb=" CB TYR K 36 " pdb=" CG TYR K 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.60e+01 bond pdb=" CB TYR J 36 " pdb=" CG TYR J 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.59e+01 ... (remaining 20200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 23734 2.53 - 5.07: 3191 5.07 - 7.60: 472 7.60 - 10.14: 38 10.14 - 12.67: 18 Bond angle restraints: 27453 Sorted by residual: angle pdb=" N SER F 613 " pdb=" CA SER F 613 " pdb=" C SER F 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER E 613 " pdb=" CA SER E 613 " pdb=" C SER E 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER B 613 " pdb=" CA SER B 613 " pdb=" C SER B 613 " ideal model delta sigma weight residual 114.62 101.97 12.65 1.14e+00 7.69e-01 1.23e+02 angle pdb=" N PHE D 53 " pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 111.36 122.40 -11.04 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 122.39 -11.03 1.09e+00 8.42e-01 1.02e+02 ... (remaining 27448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10941 17.90 - 35.80: 303 35.80 - 53.70: 132 53.70 - 71.61: 42 71.61 - 89.51: 18 Dihedral angle restraints: 11436 sinusoidal: 4572 harmonic: 6864 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 93.00 150.29 -57.29 1 1.00e+01 1.00e-02 4.41e+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 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+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 93.00 150.25 -57.25 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 11433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2574 0.113 - 0.226: 687 0.226 - 0.338: 87 0.338 - 0.451: 0 0.451 - 0.564: 6 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.33e+01 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 ... (remaining 3351 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.057 2.00e-02 2.50e+03 5.89e-02 4.34e+01 pdb=" CG ASN D 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.056 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" CG ASN C 392 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.056 2.00e-02 2.50e+03 5.87e-02 4.30e+01 pdb=" CG ASN A 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.070 2.00e-02 2.50e+03 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 335 2.61 - 3.18: 17911 3.18 - 3.75: 31236 3.75 - 4.33: 45173 4.33 - 4.90: 70376 Nonbonded interactions: 165031 Sorted by model distance: nonbonded pdb=" CZ PHE A 288 " pdb=" CD1 LEU A 452 " model vdw 2.033 3.760 nonbonded pdb=" CZ PHE C 288 " pdb=" CD1 LEU C 452 " model vdw 2.034 3.760 nonbonded pdb=" CZ PHE D 288 " pdb=" CD1 LEU D 452 " model vdw 2.035 3.760 nonbonded pdb=" OG1 THR A 357 " pdb=" OG1 THR A 465 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR C 357 " pdb=" OG1 THR C 465 " model vdw 2.314 3.040 ... (remaining 165026 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: 0.06 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 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'Z' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.830 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 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 : 0.020 0.123 20334 Z= 1.106 Angle : 1.829 12.674 27798 Z= 1.161 Chirality : 0.101 0.564 3354 Planarity : 0.009 0.049 3366 Dihedral : 10.977 89.508 6882 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 1.29 % Allowed : 4.50 % Favored : 94.22 % Rotamer: Outliers : 0.72 % Allowed : 0.57 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2334 helix: -0.19 (0.23), residues: 453 sheet: 0.58 (0.19), residues: 681 loop : -0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.045 0.010 TYR J 36 PHE 0.032 0.006 PHE I 78 TRP 0.054 0.010 TRP J 35 HIS 0.017 0.003 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.02035 / 1.10 (20205) covalent geometry : angle 1.80948 / 1.16 (27453) SS BOND : bond 0.03266 / 1.48 ( 42) SS BOND : angle 2.62598 / 1.87 ( 84) hydrogen bonds : bond 0.15268 / 9.95 ( 750) hydrogen bonds : angle 7.79749 / 5.42 ( 1953) link_ALPHA1-2 : bond 0.04223 / 2.12 ( 3) link_ALPHA1-2 : angle 2.80402 / 1.89 ( 9) link_ALPHA1-3 : bond 0.03065 / 1.54 ( 3) link_ALPHA1-3 : angle 2.37911 / 1.58 ( 9) link_ALPHA1-6 : bond 0.03640 / 1.82 ( 3) link_ALPHA1-6 : angle 3.23554 / 2.21 ( 9) link_BETA1-4 : bond 0.02857 / 1.75 ( 33) link_BETA1-4 : angle 3.93956 / 2.76 ( 99) link_NAG-ASN : bond 0.02673 / 1.65 ( 45) link_NAG-ASN : angle 2.45750 / 1.79 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 418 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8770 (mmm) cc_final: 0.8451 (mmt) REVERT: B 539 VAL cc_start: 0.9160 (t) cc_final: 0.8612 (t) REVERT: B 588 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8216 (mtt180) REVERT: L 93 ASN cc_start: 0.9074 (t0) cc_final: 0.8804 (m110) REVERT: E 539 VAL cc_start: 0.9198 (t) cc_final: 0.8770 (t) REVERT: E 586 TYR cc_start: 0.9305 (t80) cc_final: 0.9053 (t80) REVERT: E 588 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8168 (mtt180) REVERT: D 112 TRP cc_start: 0.8410 (t-100) cc_final: 0.8034 (t-100) REVERT: D 150 MET cc_start: 0.8793 (mmm) cc_final: 0.8580 (mmp) REVERT: F 588 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8112 (mtt180) REVERT: K 93 ASN cc_start: 0.9048 (t0) cc_final: 0.8830 (m-40) outliers start: 15 outliers final: 9 residues processed: 433 average time/residue: 0.1619 time to fit residues: 104.5488 Evaluate side-chains 191 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 352 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 91 HIS C 377 ASN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN J 53 ASN J 91 HIS J 92 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.059010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048406 restraints weight = 101582.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050254 restraints weight = 48930.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051518 restraints weight = 30808.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.052330 restraints weight = 22449.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052926 restraints weight = 18116.904| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20334 Z= 0.185 Angle : 0.858 12.869 27798 Z= 0.427 Chirality : 0.048 0.199 3354 Planarity : 0.004 0.038 3366 Dihedral : 5.957 50.089 2547 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.36 % Favored : 94.00 % Rotamer: Outliers : 1.91 % Allowed : 7.65 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.24 (0.17), residues: 2334 helix: 0.25 (0.24), residues: 471 sheet: 0.52 (0.19), residues: 675 loop : -0.69 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 65 TYR 0.018 0.002 TYR J 50 PHE 0.017 0.002 PHE G 78 TRP 0.036 0.002 TRP B 628 HIS 0.004 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (20205) covalent geometry : angle 0.82158 / 0.42 (27453) SS BOND : bond 0.00447 / 0.25 ( 42) SS BOND : angle 1.06205 / 0.72 ( 84) hydrogen bonds : bond 0.05520 / 3.68 ( 750) hydrogen bonds : angle 6.08026 / 4.13 ( 1953) link_ALPHA1-2 : bond 0.00414 / 0.21 ( 3) link_ALPHA1-2 : angle 1.56597 / 1.01 ( 9) link_ALPHA1-3 : bond 0.00968 / 0.47 ( 3) link_ALPHA1-3 : angle 1.82230 / 1.19 ( 9) link_ALPHA1-6 : bond 0.01348 / 0.67 ( 3) link_ALPHA1-6 : angle 1.66286 / 1.10 ( 9) link_BETA1-4 : bond 0.00340 / 0.20 ( 33) link_BETA1-4 : angle 2.50775 / 1.79 ( 99) link_NAG-ASN : bond 0.00324 / 0.20 ( 45) link_NAG-ASN : angle 2.92085 / 2.08 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9283 (ttm) cc_final: 0.9053 (ttm) REVERT: A 107 ASP cc_start: 0.9011 (m-30) cc_final: 0.8719 (t0) REVERT: A 112 TRP cc_start: 0.8201 (t-100) cc_final: 0.7753 (t-100) REVERT: A 271 MET cc_start: 0.7832 (mmm) cc_final: 0.7632 (mmm) REVERT: A 427 TRP cc_start: 0.8341 (m-90) cc_final: 0.7633 (m-90) REVERT: B 574 LYS cc_start: 0.9276 (mtmt) cc_final: 0.9013 (mtmm) REVERT: B 626 MET cc_start: 0.7663 (ttm) cc_final: 0.5859 (mtp) REVERT: H 65 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8562 (mmm160) REVERT: L 70 ASP cc_start: 0.8837 (m-30) cc_final: 0.8205 (p0) REVERT: L 93 ASN cc_start: 0.9109 (t0) cc_final: 0.8795 (m110) REVERT: C 104 MET cc_start: 0.9257 (ttm) cc_final: 0.8933 (ttm) REVERT: C 112 TRP cc_start: 0.8138 (t-100) cc_final: 0.7916 (t-100) REVERT: C 150 MET cc_start: 0.8549 (mmt) cc_final: 0.8241 (mtp) REVERT: C 381 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 427 TRP cc_start: 0.8409 (m-90) cc_final: 0.7703 (m-10) REVERT: E 626 MET cc_start: 0.7683 (ttm) cc_final: 0.4418 (mtp) REVERT: E 647 GLU cc_start: 0.8800 (pp20) cc_final: 0.8559 (tm-30) REVERT: G 72 ASP cc_start: 0.8303 (t0) cc_final: 0.8071 (t0) REVERT: D 112 TRP cc_start: 0.8120 (t-100) cc_final: 0.7893 (t-100) REVERT: D 161 MET cc_start: 0.8559 (tpt) cc_final: 0.7925 (tpt) REVERT: D 381 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: I 33 TYR cc_start: 0.8518 (m-80) cc_final: 0.8264 (m-80) REVERT: I 64 LYS cc_start: 0.9330 (pttt) cc_final: 0.9086 (ptmm) REVERT: I 65 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8577 (mmm160) REVERT: K 49 TYR cc_start: 0.9036 (p90) cc_final: 0.8715 (p90) REVERT: K 89 GLN cc_start: 0.8518 (pp30) cc_final: 0.7891 (tm-30) REVERT: K 93 ASN cc_start: 0.9112 (t0) cc_final: 0.8774 (m110) outliers start: 40 outliers final: 18 residues processed: 286 average time/residue: 0.1546 time to fit residues: 67.1844 Evaluate side-chains 203 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 230 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 0.0000 chunk 36 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 89 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS C 377 ASN G 76 ASN G 105 GLN J 89 GLN D 114 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 HIS K 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.057226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045822 restraints weight = 101414.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.047639 restraints weight = 50072.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048883 restraints weight = 32082.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049664 restraints weight = 23782.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050246 restraints weight = 19493.616| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20334 Z= 0.160 Angle : 0.760 12.308 27798 Z= 0.371 Chirality : 0.045 0.264 3354 Planarity : 0.004 0.033 3366 Dihedral : 5.451 50.799 2539 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.53 % Favored : 93.92 % Rotamer: Outliers : 1.82 % Allowed : 9.23 % Favored : 88.95 % 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: -0.18 (0.17), residues: 2334 helix: 0.83 (0.26), residues: 456 sheet: 0.40 (0.19), residues: 690 loop : -0.79 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.027 0.002 TYR K 50 PHE 0.017 0.002 PHE C 288 TRP 0.032 0.002 TRP F 571 HIS 0.008 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (20205) covalent geometry : angle 0.72764 / 0.36 (27453) SS BOND : bond 0.00375 / 0.21 ( 42) SS BOND : angle 0.84812 / 0.59 ( 84) hydrogen bonds : bond 0.04682 / 3.17 ( 750) hydrogen bonds : angle 5.63463 / 3.83 ( 1953) link_ALPHA1-2 : bond 0.00272 / 0.14 ( 3) link_ALPHA1-2 : angle 1.34959 / 0.92 ( 9) link_ALPHA1-3 : bond 0.01176 / 0.57 ( 3) link_ALPHA1-3 : angle 1.29257 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00598 / 0.30 ( 3) link_ALPHA1-6 : angle 1.30847 / 0.95 ( 9) link_BETA1-4 : bond 0.00427 / 0.25 ( 33) link_BETA1-4 : angle 2.18977 / 1.56 ( 99) link_NAG-ASN : bond 0.00288 / 0.19 ( 45) link_NAG-ASN : angle 2.66609 / 1.92 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8145 (t-100) cc_final: 0.7499 (t-100) REVERT: B 586 TYR cc_start: 0.8570 (t80) cc_final: 0.8237 (t80) REVERT: B 589 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7827 (p0) REVERT: H 46 GLU cc_start: 0.8286 (mp0) cc_final: 0.7884 (mp0) REVERT: L 70 ASP cc_start: 0.8752 (m-30) cc_final: 0.8024 (p0) REVERT: L 89 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: L 93 ASN cc_start: 0.9136 (t0) cc_final: 0.8808 (m-40) REVERT: C 104 MET cc_start: 0.9305 (ttm) cc_final: 0.8940 (ttm) REVERT: C 112 TRP cc_start: 0.8226 (t-100) cc_final: 0.7753 (t-100) REVERT: C 381 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8105 (tm-30) REVERT: C 427 TRP cc_start: 0.8133 (m-90) cc_final: 0.7712 (m-10) REVERT: E 574 LYS cc_start: 0.9319 (mtmt) cc_final: 0.9110 (mtmm) REVERT: E 584 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8589 (tm-30) REVERT: J 89 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: D 104 MET cc_start: 0.9179 (ttm) cc_final: 0.8920 (ttm) REVERT: D 112 TRP cc_start: 0.8435 (t-100) cc_final: 0.8133 (t-100) REVERT: D 122 LEU cc_start: 0.9313 (mt) cc_final: 0.8956 (pp) REVERT: D 161 MET cc_start: 0.8495 (tpt) cc_final: 0.8243 (tpt) REVERT: D 381 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: F 530 MET cc_start: 0.8556 (mtm) cc_final: 0.8104 (mtp) REVERT: F 574 LYS cc_start: 0.9288 (mtmm) cc_final: 0.8916 (ptpp) REVERT: F 656 ASN cc_start: 0.9561 (m-40) cc_final: 0.9322 (m-40) REVERT: I 29 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8918 (mm) REVERT: I 64 LYS cc_start: 0.9354 (pttt) cc_final: 0.9073 (ptmm) REVERT: I 65 ARG cc_start: 0.8876 (mmm160) cc_final: 0.8494 (mmm160) REVERT: K 49 TYR cc_start: 0.9195 (p90) cc_final: 0.8877 (p90) REVERT: K 93 ASN cc_start: 0.9151 (t0) cc_final: 0.8838 (m-40) REVERT: K 103 LYS cc_start: 0.9085 (tptm) cc_final: 0.8870 (tptp) outliers start: 38 outliers final: 14 residues processed: 237 average time/residue: 0.1617 time to fit residues: 57.9820 Evaluate side-chains 193 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 126 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 230 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.056453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.044969 restraints weight = 102935.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046749 restraints weight = 50965.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.047967 restraints weight = 32860.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048782 restraints weight = 24562.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049316 restraints weight = 20075.744| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20334 Z= 0.158 Angle : 0.712 8.380 27798 Z= 0.348 Chirality : 0.044 0.282 3354 Planarity : 0.004 0.050 3366 Dihedral : 5.237 50.218 2539 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.78 % Favored : 93.83 % Rotamer: Outliers : 1.63 % Allowed : 9.71 % Favored : 88.67 % 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: -0.09 (0.17), residues: 2334 helix: 0.86 (0.26), residues: 459 sheet: 0.58 (0.20), residues: 657 loop : -0.76 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 65 TYR 0.029 0.002 TYR K 50 PHE 0.015 0.002 PHE I 78 TRP 0.029 0.002 TRP B 571 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (20205) covalent geometry : angle 0.68239 / 0.34 (27453) SS BOND : bond 0.00350 / 0.20 ( 42) SS BOND : angle 0.74005 / 0.51 ( 84) hydrogen bonds : bond 0.04249 / 2.85 ( 750) hydrogen bonds : angle 5.31512 / 3.63 ( 1953) link_ALPHA1-2 : bond 0.00208 / 0.11 ( 3) link_ALPHA1-2 : angle 1.36239 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00494 / 0.25 ( 3) link_ALPHA1-3 : angle 1.33362 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00481 / 0.24 ( 3) link_ALPHA1-6 : angle 1.31944 / 0.96 ( 9) link_BETA1-4 : bond 0.00298 / 0.16 ( 33) link_BETA1-4 : angle 2.00464 / 1.43 ( 99) link_NAG-ASN : bond 0.00400 / 0.26 ( 45) link_NAG-ASN : angle 2.47663 / 1.87 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9416 (ptm) cc_final: 0.9180 (ppp) REVERT: A 112 TRP cc_start: 0.8179 (t-100) cc_final: 0.7628 (t-100) REVERT: A 161 MET cc_start: 0.8137 (tpt) cc_final: 0.7907 (tpt) REVERT: A 271 MET cc_start: 0.7893 (mmm) cc_final: 0.7678 (mmm) REVERT: A 426 MET cc_start: 0.8463 (ttm) cc_final: 0.8216 (ttm) REVERT: A 465 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8006 (m) REVERT: B 574 LYS cc_start: 0.9336 (mtmm) cc_final: 0.9117 (mtmm) REVERT: B 626 MET cc_start: 0.7800 (mtp) cc_final: 0.7143 (ttt) REVERT: H 46 GLU cc_start: 0.8291 (mp0) cc_final: 0.7966 (mp0) REVERT: L 70 ASP cc_start: 0.8679 (m-30) cc_final: 0.7997 (p0) REVERT: L 93 ASN cc_start: 0.9085 (t0) cc_final: 0.8779 (m-40) REVERT: C 104 MET cc_start: 0.9325 (ttm) cc_final: 0.8921 (ttm) REVERT: C 112 TRP cc_start: 0.8356 (t-100) cc_final: 0.7784 (t-100) REVERT: C 381 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 426 MET cc_start: 0.8538 (mmm) cc_final: 0.8033 (tpp) REVERT: C 465 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8106 (m) REVERT: E 574 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8988 (mtmm) REVERT: E 584 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8560 (tm-30) REVERT: G 46 GLU cc_start: 0.8525 (mp0) cc_final: 0.8214 (mp0) REVERT: J 103 LYS cc_start: 0.8909 (tptm) cc_final: 0.8692 (tptp) REVERT: D 95 MET cc_start: 0.9353 (ptm) cc_final: 0.9062 (ppp) REVERT: D 104 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9045 (ttm) REVERT: D 112 TRP cc_start: 0.8368 (t-100) cc_final: 0.7924 (t-100) REVERT: D 381 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 465 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8070 (m) REVERT: F 656 ASN cc_start: 0.9531 (m-40) cc_final: 0.9291 (m110) REVERT: I 29 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8827 (mm) REVERT: I 64 LYS cc_start: 0.9376 (pttt) cc_final: 0.9104 (ptmm) REVERT: I 65 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8513 (mmm160) REVERT: K 49 TYR cc_start: 0.9264 (p90) cc_final: 0.8797 (p90) REVERT: K 93 ASN cc_start: 0.9157 (t0) cc_final: 0.8916 (m-40) REVERT: K 103 LYS cc_start: 0.9118 (tptm) cc_final: 0.8903 (tptp) outliers start: 34 outliers final: 19 residues processed: 215 average time/residue: 0.1499 time to fit residues: 49.8672 Evaluate side-chains 197 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 227 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN J 89 GLN I 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042368 restraints weight = 105434.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044038 restraints weight = 53587.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045156 restraints weight = 35164.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.045914 restraints weight = 26773.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046417 restraints weight = 22250.023| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 20334 Z= 0.259 Angle : 0.771 10.242 27798 Z= 0.375 Chirality : 0.045 0.327 3354 Planarity : 0.005 0.078 3366 Dihedral : 5.358 54.376 2539 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.83 % Favored : 93.74 % Rotamer: Outliers : 2.01 % Allowed : 9.71 % Favored : 88.28 % 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 (0.17), residues: 2334 helix: 0.80 (0.25), residues: 459 sheet: 0.44 (0.21), residues: 615 loop : -0.86 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 65 TYR 0.030 0.002 TYR E 586 PHE 0.016 0.002 PHE G 78 TRP 0.020 0.002 TRP F 571 HIS 0.009 0.002 HIS D 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (20205) covalent geometry : angle 0.74013 / 0.37 (27453) SS BOND : bond 0.00498 / 0.32 ( 42) SS BOND : angle 0.81339 / 0.56 ( 84) hydrogen bonds : bond 0.04412 / 2.94 ( 750) hydrogen bonds : angle 5.36601 / 3.68 ( 1953) link_ALPHA1-2 : bond 0.00116 / 0.06 ( 3) link_ALPHA1-2 : angle 1.57288 / 1.11 ( 9) link_ALPHA1-3 : bond 0.00365 / 0.18 ( 3) link_ALPHA1-3 : angle 1.47137 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00603 / 0.30 ( 3) link_ALPHA1-6 : angle 1.32029 / 0.95 ( 9) link_BETA1-4 : bond 0.00287 / 0.16 ( 33) link_BETA1-4 : angle 2.03178 / 1.45 ( 99) link_NAG-ASN : bond 0.00625 / 0.41 ( 45) link_NAG-ASN : angle 2.64958 / 1.95 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8107 (tpt) cc_final: 0.7899 (tpt) REVERT: A 465 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8057 (m) REVERT: B 530 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8008 (mmm) REVERT: B 566 LEU cc_start: 0.9181 (mt) cc_final: 0.8859 (pp) REVERT: B 584 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 626 MET cc_start: 0.8278 (mtp) cc_final: 0.7510 (ttt) REVERT: L 93 ASN cc_start: 0.9127 (t0) cc_final: 0.8690 (p0) REVERT: C 104 MET cc_start: 0.9328 (ttm) cc_final: 0.8974 (ttm) REVERT: C 465 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8169 (m) REVERT: E 530 MET cc_start: 0.8892 (mtm) cc_final: 0.8659 (mtt) REVERT: E 566 LEU cc_start: 0.9297 (mt) cc_final: 0.8945 (pp) REVERT: E 574 LYS cc_start: 0.9384 (mtmt) cc_final: 0.9150 (mtmm) REVERT: E 584 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8517 (tm-30) REVERT: E 643 TYR cc_start: 0.9028 (m-10) cc_final: 0.8595 (m-80) REVERT: J 4 MET cc_start: 0.7998 (mmm) cc_final: 0.7483 (mmm) REVERT: J 89 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8538 (tm-30) REVERT: J 103 LYS cc_start: 0.8999 (tptm) cc_final: 0.8772 (tptp) REVERT: D 112 TRP cc_start: 0.8445 (t-100) cc_final: 0.8061 (t-100) REVERT: D 381 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: D 465 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8140 (m) REVERT: F 566 LEU cc_start: 0.9170 (mt) cc_final: 0.8821 (pp) REVERT: F 574 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9045 (mtmm) REVERT: F 626 MET cc_start: 0.8582 (mtp) cc_final: 0.8076 (ttt) REVERT: F 656 ASN cc_start: 0.9454 (m-40) cc_final: 0.9205 (m110) REVERT: I 29 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8732 (mm) REVERT: K 49 TYR cc_start: 0.9422 (p90) cc_final: 0.9022 (p90) REVERT: K 93 ASN cc_start: 0.9166 (t0) cc_final: 0.8961 (m-40) REVERT: K 97 THR cc_start: 0.8754 (m) cc_final: 0.8033 (p) REVERT: K 103 LYS cc_start: 0.9157 (tptm) cc_final: 0.8924 (tptp) outliers start: 42 outliers final: 18 residues processed: 206 average time/residue: 0.1413 time to fit residues: 45.3771 Evaluate side-chains 183 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 381 GLU Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 87 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 182 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044105 restraints weight = 103417.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045845 restraints weight = 51365.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.047012 restraints weight = 33282.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047763 restraints weight = 25001.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048313 restraints weight = 20669.610| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20334 Z= 0.121 Angle : 0.671 9.255 27798 Z= 0.325 Chirality : 0.044 0.334 3354 Planarity : 0.003 0.054 3366 Dihedral : 4.928 44.429 2531 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.48 % Favored : 94.00 % Rotamer: Outliers : 1.34 % Allowed : 10.71 % Favored : 87.95 % 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: -0.22 (0.18), residues: 2334 helix: 0.87 (0.25), residues: 462 sheet: 0.50 (0.20), residues: 684 loop : -0.94 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 65 TYR 0.033 0.002 TYR B 643 PHE 0.012 0.001 PHE G 78 TRP 0.022 0.001 TRP B 596 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (20205) covalent geometry : angle 0.64630 / 0.32 (27453) SS BOND : bond 0.00248 / 0.13 ( 42) SS BOND : angle 0.62419 / 0.45 ( 84) hydrogen bonds : bond 0.03780 / 2.55 ( 750) hydrogen bonds : angle 5.03974 / 3.46 ( 1953) link_ALPHA1-2 : bond 0.00281 / 0.14 ( 3) link_ALPHA1-2 : angle 1.35611 / 0.95 ( 9) link_ALPHA1-3 : bond 0.00554 / 0.28 ( 3) link_ALPHA1-3 : angle 1.48414 / 1.10 ( 9) link_ALPHA1-6 : bond 0.00568 / 0.28 ( 3) link_ALPHA1-6 : angle 1.33532 / 0.95 ( 9) link_BETA1-4 : bond 0.00356 / 0.20 ( 33) link_BETA1-4 : angle 1.80901 / 1.30 ( 99) link_NAG-ASN : bond 0.00414 / 0.24 ( 45) link_NAG-ASN : angle 2.20514 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8964 (ttm) REVERT: A 122 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9284 (pp) REVERT: A 271 MET cc_start: 0.8165 (mmm) cc_final: 0.7838 (mmm) REVERT: A 465 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7950 (m) REVERT: B 530 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7403 (mmm) REVERT: B 566 LEU cc_start: 0.9169 (mt) cc_final: 0.8832 (pp) REVERT: B 574 LYS cc_start: 0.9307 (mtmm) cc_final: 0.8981 (mtmm) REVERT: B 584 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 626 MET cc_start: 0.8178 (mtp) cc_final: 0.7493 (ttt) REVERT: L 93 ASN cc_start: 0.9122 (t0) cc_final: 0.8716 (m-40) REVERT: C 104 MET cc_start: 0.9328 (ttm) cc_final: 0.8955 (ttm) REVERT: C 112 TRP cc_start: 0.8645 (t-100) cc_final: 0.8098 (t-100) REVERT: C 150 MET cc_start: 0.8840 (mtp) cc_final: 0.8579 (mtp) REVERT: C 465 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8060 (m) REVERT: E 566 LEU cc_start: 0.9168 (mt) cc_final: 0.8854 (pp) REVERT: E 574 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9162 (mtmm) REVERT: E 584 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8525 (tm-30) REVERT: E 586 TYR cc_start: 0.9014 (t80) cc_final: 0.8489 (t80) REVERT: E 643 TYR cc_start: 0.8990 (m-10) cc_final: 0.8599 (m-80) REVERT: G 102 TYR cc_start: 0.8949 (m-80) cc_final: 0.8636 (m-10) REVERT: J 103 LYS cc_start: 0.9017 (tptm) cc_final: 0.8793 (tptp) REVERT: D 104 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8880 (ttm) REVERT: D 112 TRP cc_start: 0.8240 (t-100) cc_final: 0.7779 (t-100) REVERT: D 465 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8065 (m) REVERT: F 566 LEU cc_start: 0.9142 (mt) cc_final: 0.8832 (pp) REVERT: F 574 LYS cc_start: 0.9183 (mtmm) cc_final: 0.8840 (mtmm) REVERT: F 584 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8510 (tm-30) REVERT: F 596 TRP cc_start: 0.9036 (m-10) cc_final: 0.8578 (m-90) REVERT: F 626 MET cc_start: 0.8658 (mtp) cc_final: 0.8101 (ttt) REVERT: F 656 ASN cc_start: 0.9474 (m-40) cc_final: 0.9231 (m110) REVERT: I 29 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8700 (mm) REVERT: K 49 TYR cc_start: 0.9305 (p90) cc_final: 0.8997 (p90) REVERT: K 93 ASN cc_start: 0.9167 (t0) cc_final: 0.8846 (m-40) REVERT: K 103 LYS cc_start: 0.9141 (tptm) cc_final: 0.8920 (tptp) outliers start: 28 outliers final: 14 residues processed: 210 average time/residue: 0.1484 time to fit residues: 47.6953 Evaluate side-chains 197 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 220 optimal weight: 0.0170 chunk 212 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 overall best weight: 3.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN H 13 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN J 92 ASN K 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.053237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.041615 restraints weight = 106370.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043253 restraints weight = 53883.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044357 restraints weight = 35393.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045086 restraints weight = 26924.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045545 restraints weight = 22425.140| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20334 Z= 0.268 Angle : 0.750 10.613 27798 Z= 0.366 Chirality : 0.045 0.333 3354 Planarity : 0.005 0.080 3366 Dihedral : 5.124 47.678 2531 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.13 % Favored : 93.27 % Rotamer: Outliers : 1.72 % Allowed : 11.43 % Favored : 86.85 % 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: -0.40 (0.17), residues: 2334 helix: 0.73 (0.25), residues: 465 sheet: 0.47 (0.21), residues: 645 loop : -1.08 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 65 TYR 0.047 0.002 TYR B 643 PHE 0.018 0.002 PHE C 382 TRP 0.022 0.002 TRP B 571 HIS 0.007 0.002 HIS D 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (20205) covalent geometry : angle 0.72424 / 0.36 (27453) SS BOND : bond 0.00487 / 0.30 ( 42) SS BOND : angle 0.74116 / 0.52 ( 84) hydrogen bonds : bond 0.04245 / 2.84 ( 750) hydrogen bonds : angle 5.20905 / 3.58 ( 1953) link_ALPHA1-2 : bond 0.00156 / 0.08 ( 3) link_ALPHA1-2 : angle 1.65657 / 1.19 ( 9) link_ALPHA1-3 : bond 0.00277 / 0.14 ( 3) link_ALPHA1-3 : angle 1.42801 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00571 / 0.29 ( 3) link_ALPHA1-6 : angle 1.29107 / 0.91 ( 9) link_BETA1-4 : bond 0.00270 / 0.15 ( 33) link_BETA1-4 : angle 1.93335 / 1.37 ( 99) link_NAG-ASN : bond 0.00664 / 0.43 ( 45) link_NAG-ASN : angle 2.40476 / 1.73 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8099 (m) REVERT: B 566 LEU cc_start: 0.9165 (mt) cc_final: 0.8810 (pp) REVERT: B 584 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 586 TYR cc_start: 0.8704 (t80) cc_final: 0.8477 (t80) REVERT: L 93 ASN cc_start: 0.9067 (t0) cc_final: 0.8785 (t0) REVERT: C 53 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: C 104 MET cc_start: 0.9367 (ttm) cc_final: 0.8975 (ttm) REVERT: C 150 MET cc_start: 0.8865 (mtp) cc_final: 0.8641 (mtp) REVERT: C 465 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (m) REVERT: E 566 LEU cc_start: 0.9188 (mt) cc_final: 0.8914 (pp) REVERT: E 571 TRP cc_start: 0.9026 (m-90) cc_final: 0.8393 (m-90) REVERT: E 574 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9104 (mtmm) REVERT: E 584 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8533 (tm-30) REVERT: E 586 TYR cc_start: 0.8890 (t80) cc_final: 0.8500 (t80) REVERT: E 643 TYR cc_start: 0.9044 (m-10) cc_final: 0.8843 (m-80) REVERT: J 103 LYS cc_start: 0.9037 (tptm) cc_final: 0.8801 (tptp) REVERT: D 95 MET cc_start: 0.9360 (ptm) cc_final: 0.9043 (ppp) REVERT: D 112 TRP cc_start: 0.8584 (t-100) cc_final: 0.8233 (t-100) REVERT: D 465 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8167 (m) REVERT: F 566 LEU cc_start: 0.9144 (mt) cc_final: 0.8785 (pp) REVERT: F 574 LYS cc_start: 0.9286 (mtmm) cc_final: 0.8982 (mtmm) REVERT: F 656 ASN cc_start: 0.9446 (m-40) cc_final: 0.9192 (m110) REVERT: K 49 TYR cc_start: 0.9428 (p90) cc_final: 0.9117 (p90) REVERT: K 93 ASN cc_start: 0.9149 (t0) cc_final: 0.8854 (t0) REVERT: K 103 LYS cc_start: 0.9196 (tptm) cc_final: 0.8953 (tptp) outliers start: 36 outliers final: 25 residues processed: 190 average time/residue: 0.1449 time to fit residues: 42.9881 Evaluate side-chains 189 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 105 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN J 92 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.053640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042143 restraints weight = 104988.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.043798 restraints weight = 52447.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.044915 restraints weight = 34099.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.045643 restraints weight = 25739.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046140 restraints weight = 21376.365| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20334 Z= 0.190 Angle : 0.696 9.569 27798 Z= 0.339 Chirality : 0.044 0.323 3354 Planarity : 0.004 0.074 3366 Dihedral : 5.056 47.640 2531 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.91 % Favored : 93.44 % Rotamer: Outliers : 1.48 % Allowed : 11.81 % Favored : 86.70 % 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: -0.41 (0.17), residues: 2334 helix: 0.77 (0.25), residues: 465 sheet: 0.56 (0.21), residues: 639 loop : -1.17 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 65 TYR 0.051 0.002 TYR B 643 PHE 0.014 0.002 PHE G 78 TRP 0.025 0.002 TRP B 571 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (20205) covalent geometry : angle 0.67106 / 0.33 (27453) SS BOND : bond 0.00358 / 0.22 ( 42) SS BOND : angle 0.66265 / 0.47 ( 84) hydrogen bonds : bond 0.03925 / 2.63 ( 750) hydrogen bonds : angle 5.08801 / 3.51 ( 1953) link_ALPHA1-2 : bond 0.00165 / 0.08 ( 3) link_ALPHA1-2 : angle 1.47235 / 1.05 ( 9) link_ALPHA1-3 : bond 0.00394 / 0.20 ( 3) link_ALPHA1-3 : angle 1.43834 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00573 / 0.29 ( 3) link_ALPHA1-6 : angle 1.28814 / 0.91 ( 9) link_BETA1-4 : bond 0.00246 / 0.13 ( 33) link_BETA1-4 : angle 1.82734 / 1.30 ( 99) link_NAG-ASN : bond 0.00450 / 0.29 ( 45) link_NAG-ASN : angle 2.23840 / 1.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: A 104 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9007 (ttm) REVERT: A 465 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7993 (m) REVERT: B 566 LEU cc_start: 0.9189 (mt) cc_final: 0.8850 (pp) REVERT: B 574 LYS cc_start: 0.9423 (mtmm) cc_final: 0.8676 (pttm) REVERT: B 584 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 626 MET cc_start: 0.8333 (mtp) cc_final: 0.7849 (ttt) REVERT: L 3 VAL cc_start: 0.9359 (t) cc_final: 0.9100 (p) REVERT: L 93 ASN cc_start: 0.9031 (t0) cc_final: 0.8772 (t0) REVERT: C 53 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: C 104 MET cc_start: 0.9375 (ttm) cc_final: 0.8948 (ttm) REVERT: C 150 MET cc_start: 0.8819 (mtp) cc_final: 0.8588 (mtp) REVERT: E 566 LEU cc_start: 0.9178 (mt) cc_final: 0.8839 (pp) REVERT: E 571 TRP cc_start: 0.8982 (m-90) cc_final: 0.8378 (m-90) REVERT: E 574 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9043 (mtmm) REVERT: E 584 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8539 (tm-30) REVERT: G 65 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8460 (mmm160) REVERT: J 89 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: J 103 LYS cc_start: 0.9009 (tptm) cc_final: 0.8780 (tptp) REVERT: D 104 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8955 (ttm) REVERT: D 112 TRP cc_start: 0.8512 (t-100) cc_final: 0.8163 (t-100) REVERT: D 426 MET cc_start: 0.8646 (ttm) cc_final: 0.8286 (ptm) REVERT: D 465 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8135 (m) REVERT: F 566 LEU cc_start: 0.9130 (mt) cc_final: 0.8801 (pp) REVERT: F 584 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8594 (tm-30) REVERT: F 656 ASN cc_start: 0.9472 (m-40) cc_final: 0.9237 (m110) REVERT: K 49 TYR cc_start: 0.9400 (p90) cc_final: 0.9095 (p90) REVERT: K 93 ASN cc_start: 0.9116 (t0) cc_final: 0.8810 (t0) REVERT: K 97 THR cc_start: 0.8902 (m) cc_final: 0.8120 (p) REVERT: K 103 LYS cc_start: 0.9174 (tptm) cc_final: 0.8950 (tptp) outliers start: 31 outliers final: 23 residues processed: 187 average time/residue: 0.1412 time to fit residues: 41.3569 Evaluate side-chains 185 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 89 GLN Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 66 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.042807 restraints weight = 105398.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.044478 restraints weight = 52940.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045574 restraints weight = 34538.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046334 restraints weight = 26232.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046803 restraints weight = 21746.634| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20334 Z= 0.145 Angle : 0.672 9.973 27798 Z= 0.327 Chirality : 0.044 0.307 3354 Planarity : 0.004 0.049 3366 Dihedral : 4.952 47.397 2531 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.87 % Favored : 93.49 % Rotamer: Outliers : 1.39 % Allowed : 11.96 % Favored : 86.66 % 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: -0.45 (0.17), residues: 2334 helix: 0.65 (0.25), residues: 462 sheet: 0.45 (0.20), residues: 678 loop : -1.13 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 65 TYR 0.063 0.002 TYR E 643 PHE 0.013 0.001 PHE H 78 TRP 0.069 0.002 TRP B 571 HIS 0.012 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (20205) covalent geometry : angle 0.65014 / 0.32 (27453) SS BOND : bond 0.00283 / 0.17 ( 42) SS BOND : angle 0.68380 / 0.48 ( 84) hydrogen bonds : bond 0.03774 / 2.51 ( 750) hydrogen bonds : angle 4.99626 / 3.43 ( 1953) link_ALPHA1-2 : bond 0.00392 / 0.20 ( 3) link_ALPHA1-2 : angle 1.49058 / 1.06 ( 9) link_ALPHA1-3 : bond 0.00474 / 0.24 ( 3) link_ALPHA1-3 : angle 1.42893 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00546 / 0.27 ( 3) link_ALPHA1-6 : angle 1.31929 / 0.92 ( 9) link_BETA1-4 : bond 0.00316 / 0.17 ( 33) link_BETA1-4 : angle 1.76571 / 1.26 ( 99) link_NAG-ASN : bond 0.00347 / 0.21 ( 45) link_NAG-ASN : angle 2.03289 / 1.46 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: A 104 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9011 (ttm) REVERT: A 112 TRP cc_start: 0.8550 (t-100) cc_final: 0.8314 (t-100) REVERT: A 115 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 465 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (m) REVERT: B 566 LEU cc_start: 0.9154 (mt) cc_final: 0.8802 (pp) REVERT: B 574 LYS cc_start: 0.9415 (mtmm) cc_final: 0.8820 (mtmm) REVERT: B 584 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 626 MET cc_start: 0.8344 (mtp) cc_final: 0.7871 (ttt) REVERT: L 3 VAL cc_start: 0.9350 (t) cc_final: 0.9097 (p) REVERT: L 93 ASN cc_start: 0.9056 (t0) cc_final: 0.8807 (t0) REVERT: C 53 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: C 95 MET cc_start: 0.9632 (ppp) cc_final: 0.9394 (ppp) REVERT: C 100 MET cc_start: 0.9123 (mtm) cc_final: 0.8893 (mtm) REVERT: C 104 MET cc_start: 0.9350 (ttm) cc_final: 0.8951 (ttm) REVERT: C 150 MET cc_start: 0.8834 (mtp) cc_final: 0.8600 (mtp) REVERT: C 426 MET cc_start: 0.8301 (ttp) cc_final: 0.7764 (ttm) REVERT: E 571 TRP cc_start: 0.9005 (m-90) cc_final: 0.8388 (m-90) REVERT: E 574 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9024 (mtmm) REVERT: E 584 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8527 (tm-30) REVERT: E 656 ASN cc_start: 0.9415 (m-40) cc_final: 0.9155 (m-40) REVERT: G 65 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8494 (mmm160) REVERT: G 102 TYR cc_start: 0.8985 (m-80) cc_final: 0.8646 (m-10) REVERT: J 103 LYS cc_start: 0.9026 (tptm) cc_final: 0.8794 (tptp) REVERT: D 104 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8939 (ttm) REVERT: D 465 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8116 (m) REVERT: F 566 LEU cc_start: 0.9093 (mt) cc_final: 0.8750 (pp) REVERT: F 574 LYS cc_start: 0.9261 (mtmm) cc_final: 0.9035 (mtmm) REVERT: F 584 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8563 (tm-30) REVERT: F 626 MET cc_start: 0.8671 (mtp) cc_final: 0.8235 (ttt) REVERT: F 656 ASN cc_start: 0.9458 (m-40) cc_final: 0.9225 (m110) REVERT: K 49 TYR cc_start: 0.9383 (p90) cc_final: 0.9108 (p90) REVERT: K 93 ASN cc_start: 0.9091 (t0) cc_final: 0.8838 (t0) REVERT: K 97 THR cc_start: 0.8882 (m) cc_final: 0.8105 (p) REVERT: K 103 LYS cc_start: 0.9162 (tptm) cc_final: 0.8917 (tptp) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 0.1496 time to fit residues: 43.0965 Evaluate side-chains 189 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041373 restraints weight = 107260.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042981 restraints weight = 54177.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044064 restraints weight = 35683.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044773 restraints weight = 27200.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045223 restraints weight = 22764.119| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 20334 Z= 0.263 Angle : 0.758 10.507 27798 Z= 0.372 Chirality : 0.045 0.313 3354 Planarity : 0.004 0.075 3366 Dihedral : 5.180 49.375 2531 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.81 % Favored : 92.50 % Rotamer: Outliers : 1.67 % Allowed : 12.05 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.17), residues: 2334 helix: 0.54 (0.25), residues: 462 sheet: 0.54 (0.21), residues: 633 loop : -1.24 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 65 TYR 0.072 0.002 TYR E 643 PHE 0.016 0.002 PHE H 78 TRP 0.061 0.002 TRP B 571 HIS 0.006 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (20205) covalent geometry : angle 0.73507 / 0.37 (27453) SS BOND : bond 0.00481 / 0.30 ( 42) SS BOND : angle 0.82259 / 0.57 ( 84) hydrogen bonds : bond 0.04150 / 2.79 ( 750) hydrogen bonds : angle 5.17968 / 3.57 ( 1953) link_ALPHA1-2 : bond 0.00124 / 0.06 ( 3) link_ALPHA1-2 : angle 1.45814 / 1.04 ( 9) link_ALPHA1-3 : bond 0.00301 / 0.15 ( 3) link_ALPHA1-3 : angle 1.39385 / 0.99 ( 9) link_ALPHA1-6 : bond 0.00539 / 0.27 ( 3) link_ALPHA1-6 : angle 1.28435 / 0.90 ( 9) link_BETA1-4 : bond 0.00252 / 0.15 ( 33) link_BETA1-4 : angle 1.84717 / 1.31 ( 99) link_NAG-ASN : bond 0.00605 / 0.40 ( 45) link_NAG-ASN : angle 2.27893 / 1.63 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 465 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 566 LEU cc_start: 0.9138 (mt) cc_final: 0.8723 (pp) REVERT: B 574 LYS cc_start: 0.9472 (mtmm) cc_final: 0.8910 (mtmm) REVERT: B 584 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8433 (tm-30) REVERT: B 626 MET cc_start: 0.8353 (mtp) cc_final: 0.7824 (ttt) REVERT: B 656 ASN cc_start: 0.9461 (m-40) cc_final: 0.9198 (m-40) REVERT: L 3 VAL cc_start: 0.9374 (t) cc_final: 0.9117 (p) REVERT: L 93 ASN cc_start: 0.9059 (t0) cc_final: 0.8803 (t0) REVERT: C 53 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: C 104 MET cc_start: 0.9388 (ttm) cc_final: 0.8984 (ttm) REVERT: C 150 MET cc_start: 0.8874 (mtp) cc_final: 0.8512 (mtp) REVERT: C 426 MET cc_start: 0.8456 (ttp) cc_final: 0.8163 (ttm) REVERT: E 566 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8808 (pp) REVERT: E 571 TRP cc_start: 0.9095 (m-90) cc_final: 0.8466 (m-90) REVERT: E 574 LYS cc_start: 0.9419 (mtmt) cc_final: 0.9096 (mtmm) REVERT: E 584 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8532 (tm-30) REVERT: E 643 TYR cc_start: 0.9021 (m-80) cc_final: 0.8783 (m-80) REVERT: J 97 THR cc_start: 0.8859 (m) cc_final: 0.8300 (p) REVERT: J 103 LYS cc_start: 0.9043 (tptm) cc_final: 0.8794 (tptp) REVERT: D 104 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8915 (ttm) REVERT: D 465 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8152 (m) REVERT: F 566 LEU cc_start: 0.9110 (mt) cc_final: 0.8792 (pp) REVERT: F 574 LYS cc_start: 0.9264 (mtmm) cc_final: 0.8838 (pttm) REVERT: F 584 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8573 (tm-30) REVERT: F 656 ASN cc_start: 0.9454 (m-40) cc_final: 0.9233 (m110) REVERT: I 65 ARG cc_start: 0.8995 (mmm160) cc_final: 0.8721 (mmm160) REVERT: K 49 TYR cc_start: 0.9469 (p90) cc_final: 0.9188 (p90) REVERT: K 93 ASN cc_start: 0.9119 (t0) cc_final: 0.8873 (t0) REVERT: K 97 THR cc_start: 0.9001 (m) cc_final: 0.8275 (p) REVERT: K 103 LYS cc_start: 0.9192 (tptm) cc_final: 0.8945 (tptp) outliers start: 35 outliers final: 21 residues processed: 177 average time/residue: 0.1517 time to fit residues: 41.6847 Evaluate side-chains 180 residues out of total 2091 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.052654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041041 restraints weight = 107425.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042628 restraints weight = 54547.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.043685 restraints weight = 36031.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044397 restraints weight = 27576.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044842 restraints weight = 23075.233| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 20334 Z= 0.280 Angle : 0.786 12.206 27798 Z= 0.383 Chirality : 0.046 0.285 3354 Planarity : 0.004 0.084 3366 Dihedral : 5.313 50.636 2531 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.73 % Favored : 92.54 % Rotamer: Outliers : 1.43 % Allowed : 12.63 % Favored : 85.94 % 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: -0.71 (0.17), residues: 2334 helix: 0.45 (0.24), residues: 462 sheet: 0.44 (0.21), residues: 651 loop : -1.37 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 65 TYR 0.054 0.002 TYR E 643 PHE 0.020 0.002 PHE C 382 TRP 0.078 0.002 TRP F 571 HIS 0.018 0.002 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.28 (20205) covalent geometry : angle 0.76291 / 0.38 (27453) SS BOND : bond 0.00526 / 0.32 ( 42) SS BOND : angle 0.84905 / 0.58 ( 84) hydrogen bonds : bond 0.04221 / 2.82 ( 750) hydrogen bonds : angle 5.29257 / 3.66 ( 1953) link_ALPHA1-2 : bond 0.00076 / 0.04 ( 3) link_ALPHA1-2 : angle 1.53940 / 1.12 ( 9) link_ALPHA1-3 : bond 0.00290 / 0.14 ( 3) link_ALPHA1-3 : angle 1.41600 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00548 / 0.28 ( 3) link_ALPHA1-6 : angle 1.25891 / 0.87 ( 9) link_BETA1-4 : bond 0.00245 / 0.16 ( 33) link_BETA1-4 : angle 1.82452 / 1.29 ( 99) link_NAG-ASN : bond 0.00609 / 0.40 ( 45) link_NAG-ASN : angle 2.36564 / 1.68 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.57 seconds wall clock time: 50 minutes 55.33 seconds (3055.33 seconds total)