Starting phenix.real_space_refine on Sun Sep 13 02:34:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.map" model { file = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oro_20176/09_2026/6oro_20176.cif" } resolution = 3.9 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= 0.213 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 12543 2.51 5 N 3345 2.21 5 O 4077 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 20085 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "I" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3540 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 806 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "M" 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: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 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: "W" 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: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: 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: 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: "f" 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: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.15, per 1000 atoms: 0.21 Number of scatterers: 20085 At special positions: 0 Unit cell: (143.6, 132.112, 153.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4077 8.00 N 3345 7.00 C 12543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=3, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 620 " - " ASN B 88 " " NAG B 625 " - " ASN B 339 " " NAG B 626 " - " ASN B 355 " " NAG B 629 " - " ASN B 276 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 618 " " NAG G 620 " - " ASN G 88 " " NAG G 625 " - " ASN G 339 " " NAG G 626 " - " ASN G 355 " " NAG G 629 " - " ASN G 276 " " NAG I 620 " - " ASN I 88 " " NAG I 625 " - " ASN I 339 " " NAG I 626 " - " ASN I 355 " " NAG I 629 " - " ASN I 276 " " NAG M 1 " - " ASN B 160 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 448 " " NAG Q 1 " - " ASN B 295 " " NAG R 1 " - " ASN B 197 " " NAG S 1 " - " ASN B 392 " " NAG T 1 " - " ASN B 386 " " NAG U 1 " - " ASN B 301 " " NAG V 1 " - " ASN G 160 " " NAG W 1 " - " ASN G 332 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 448 " " NAG Z 1 " - " ASN G 295 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN G 392 " " NAG c 1 " - " ASN G 386 " " NAG d 1 " - " ASN G 301 " " NAG e 1 " - " ASN I 160 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 262 " " NAG h 1 " - " ASN I 448 " " NAG i 1 " - " ASN I 295 " " NAG j 1 " - " ASN I 197 " " NAG k 1 " - " ASN I 392 " " NAG l 1 " - " ASN I 386 " " NAG m 1 " - " ASN I 301 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 684.9 milliseconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 42 sheets defined 15.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.724A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.774A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 588 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.730A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 624' Processing helix chain 'A' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS B 117 " --> pdb=" O GLN B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP B 477 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 3.776A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.528A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 581 " --> pdb=" O GLN C 577 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 588 " --> pdb=" O GLU C 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.731A pdb=" N TRP C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 624' Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.437A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.527A pdb=" N LYS C 655 " --> pdb=" O ASN C 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.725A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 3.775A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.527A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.618A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.438A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 649 removed outlier: 4.356A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 659 removed outlier: 3.526A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 113 removed outlier: 3.739A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP G 113 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.535A pdb=" N LYS G 117 " --> pdb=" O GLN G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.134A pdb=" N MET G 150 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG G 151 " --> pdb=" O SER G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 151' Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 353 removed outlier: 3.570A pdb=" N PHE G 353 " --> pdb=" O ARG G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 350 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.617A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 113 removed outlier: 3.740A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP I 113 " --> pdb=" O ILE I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.536A pdb=" N LYS I 117 " --> pdb=" O GLN I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 349 removed outlier: 3.670A pdb=" N GLU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN I 348 " --> pdb=" O LYS I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 353 removed outlier: 3.571A pdb=" N PHE I 353 " --> pdb=" O ARG I 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 350 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.616A pdb=" N THR I 372 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 373' Processing helix chain 'I' and resid 474 through 480 removed outlier: 3.711A pdb=" N ASP I 477 " --> pdb=" O ASP I 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.590A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 495 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.124A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 239 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE B 159 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.281A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 308 removed outlier: 3.510A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 307 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.573A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 495 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 81 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR D 68 " --> pdb=" O GLN D 81 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER E 67 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.970A pdb=" N CYS E 88 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 90 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 97 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.575A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY I 495 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE G 159 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 297 through 298 removed outlier: 3.740A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 304 through 307 removed outlier: 3.511A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE G 307 " --> pdb=" O PHE G 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 329 through 333 removed outlier: 3.883A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.901A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.845A pdb=" N LYS I 487 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.125A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 169 through 175 removed outlier: 3.603A pdb=" N PHE I 159 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 259 through 261 removed outlier: 4.280A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 284 through 286 removed outlier: 6.750A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 297 through 298 removed outlier: 3.739A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.511A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE I 307 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 329 through 333 removed outlier: 3.882A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.505A pdb=" N THR J 77 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN J 81 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR J 68 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.902A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.910A pdb=" N SER K 67 " --> pdb=" O THR K 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 88 through 91 removed outlier: 3.969A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL K 90 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU K 97 " --> pdb=" O VAL K 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.911A pdb=" N SER L 67 " --> pdb=" O THR L 70 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.968A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL L 90 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU L 97 " --> pdb=" O VAL L 90 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 936 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: 3.24 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3214 1.26 - 1.40: 4782 1.40 - 1.54: 12093 1.54 - 1.68: 230 1.68 - 1.82: 162 Bond restraints: 20481 Sorted by residual: bond pdb=" C ASN F 618 " pdb=" O ASN F 618 " ideal model delta sigma weight residual 1.233 1.118 0.115 1.36e-02 5.41e+03 7.13e+01 bond pdb=" C ASN F 618 " pdb=" N LEU F 619 " ideal model delta sigma weight residual 1.332 1.218 0.114 1.40e-02 5.10e+03 6.62e+01 bond pdb=" C ILE B 309 " pdb=" O ILE B 309 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.19e-02 7.06e+03 4.17e+01 bond pdb=" C ILE G 309 " pdb=" O ILE G 309 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C ALA I 316 " pdb=" O ALA I 316 " ideal model delta sigma weight residual 1.233 1.163 0.071 1.28e-02 6.10e+03 3.05e+01 ... (remaining 20476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 27098 3.50 - 6.99: 597 6.99 - 10.49: 77 10.49 - 13.99: 22 13.99 - 17.48: 4 Bond angle restraints: 27798 Sorted by residual: angle pdb=" CA PRO G 313 " pdb=" N PRO G 313 " pdb=" CD PRO G 313 " ideal model delta sigma weight residual 111.50 96.11 15.39 1.40e+00 5.10e-01 1.21e+02 angle pdb=" CA PRO B 313 " pdb=" N PRO B 313 " pdb=" CD PRO B 313 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.40e+00 5.10e-01 7.76e+01 angle pdb=" CA PRO I 313 " pdb=" N PRO I 313 " pdb=" CD PRO I 313 " ideal model delta sigma weight residual 111.50 99.85 11.65 1.40e+00 5.10e-01 6.92e+01 angle pdb=" N PRO B 136 " pdb=" CA PRO B 136 " pdb=" C PRO B 136 " ideal model delta sigma weight residual 113.47 101.67 11.80 1.43e+00 4.89e-01 6.81e+01 angle pdb=" N PRO I 136 " pdb=" CA PRO I 136 " pdb=" C PRO I 136 " ideal model delta sigma weight residual 113.47 102.44 11.03 1.43e+00 4.89e-01 5.95e+01 ... (remaining 27793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 10736 16.63 - 33.25: 538 33.25 - 49.88: 144 49.88 - 66.51: 35 66.51 - 83.14: 31 Dihedral angle restraints: 11484 sinusoidal: 4575 harmonic: 6909 Sorted by residual: dihedral pdb=" CA ASN C 637 " pdb=" C ASN C 637 " pdb=" N TYR C 638 " pdb=" CA TYR C 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN A 637 " pdb=" C ASN A 637 " pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta harmonic sigma weight residual 180.00 130.97 49.03 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ASN F 637 " pdb=" C ASN F 637 " pdb=" N TYR F 638 " pdb=" CA TYR F 638 " ideal model delta harmonic sigma weight residual 180.00 130.99 49.01 0 5.00e+00 4.00e-02 9.61e+01 ... (remaining 11481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 3355 0.302 - 0.604: 15 0.604 - 0.907: 3 0.907 - 1.209: 0 1.209 - 1.511: 2 Chirality restraints: 3375 Sorted by residual: chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 618 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.71e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-01 2.50e+01 5.70e+01 chirality pdb=" C1 NAG B 629 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 629 " pdb=" O5 NAG B 629 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.59e+01 ... (remaining 3372 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 617 " -0.030 2.00e-02 2.50e+03 6.10e-02 3.73e+01 pdb=" C ARG F 617 " 0.106 2.00e-02 2.50e+03 pdb=" O ARG F 617 " -0.039 2.00e-02 2.50e+03 pdb=" N ASN F 618 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 309 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.25e+01 pdb=" C ILE B 309 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE B 309 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY B 312 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.049 2.00e-02 2.50e+03 4.05e-02 2.05e+01 pdb=" C7 NAG F 703 " 0.000 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.068 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.012 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 313 2.62 - 3.19: 16485 3.19 - 3.76: 27050 3.76 - 4.33: 35037 4.33 - 4.90: 58333 Nonbonded interactions: 137218 Sorted by model distance: nonbonded pdb=" O4 NAG F 703 " pdb=" O6 NAG F 703 " model vdw 2.048 3.040 nonbonded pdb=" OE2 GLU C 621 " pdb=" C5 NAG C 702 " model vdw 2.220 3.470 nonbonded pdb=" OE2 GLU A 621 " pdb=" C5 NAG A 702 " model vdw 2.220 3.470 nonbonded pdb=" O VAL H 12 " pdb=" OG SER H 112 " model vdw 2.263 3.040 nonbonded pdb=" O VAL J 12 " pdb=" OG SER J 112 " model vdw 2.263 3.040 ... (remaining 137213 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'X' selection = chain 'g' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.330 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.009 0.115 20613 Z= 0.448 Angle : 1.425 23.895 28152 Z= 0.727 Chirality : 0.087 1.511 3375 Planarity : 0.008 0.084 3432 Dihedral : 11.964 80.593 6945 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.59 % Allowed : 13.05 % Favored : 86.35 % Rotamer: Outliers : 2.93 % Allowed : 2.64 % Favored : 94.44 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.92 % 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: -5.30 (0.13), residues: 2367 helix: -4.63 (0.15), residues: 330 sheet: -3.26 (0.20), residues: 465 loop : -3.56 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 308 TYR 0.043 0.003 TYR I 134 PHE 0.039 0.003 PHE J 100C TRP 0.035 0.004 TRP H 47 HIS 0.011 0.002 HIS L 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.45 (20481) covalent geometry : angle 1.31879 / 0.71 (27798) SS BOND : bond 0.00665 / 0.41 ( 33) SS BOND : angle 1.57935 / 1.10 ( 66) hydrogen bonds : bond 0.30203 / 19.94 ( 367) hydrogen bonds : angle 10.02526 / 7.03 ( 936) Misc. bond : bond 0.00040 / 0.02 ( 3) link_ALPHA1-2 : bond 0.01588 / 0.72 ( 6) link_ALPHA1-2 : angle 3.52757 / 2.43 ( 18) link_ALPHA1-3 : bond 0.00222 / 0.10 ( 3) link_ALPHA1-3 : angle 4.14878 / 2.33 ( 9) link_ALPHA1-6 : bond 0.00262 / 0.12 ( 3) link_ALPHA1-6 : angle 1.73647 / 0.81 ( 9) link_BETA1-4 : bond 0.01456 / 0.87 ( 36) link_BETA1-4 : angle 4.43551 / 2.78 ( 108) link_NAG-ASN : bond 0.01474 / 0.73 ( 48) link_NAG-ASN : angle 6.50333 / 4.56 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 580 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9189 (mttp) cc_final: 0.8868 (mtmm) REVERT: A 640 GLN cc_start: 0.9037 (mm110) cc_final: 0.8825 (mm-40) REVERT: B 92 GLU cc_start: 0.5024 (pt0) cc_final: 0.4754 (pt0) REVERT: B 95 MET cc_start: 0.8690 (ptm) cc_final: 0.8424 (ptt) REVERT: B 114 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: B 161 MET cc_start: 0.8354 (tpp) cc_final: 0.7879 (tpt) REVERT: B 356 ASN cc_start: 0.9183 (t0) cc_final: 0.8980 (t0) REVERT: B 432 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8479 (tp-100) REVERT: B 466 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: C 625 ASN cc_start: 0.8945 (m-40) cc_final: 0.8733 (m-40) REVERT: C 635 ILE cc_start: 0.9296 (tt) cc_final: 0.9000 (tt) REVERT: C 647 GLU cc_start: 0.9068 (pp20) cc_final: 0.8769 (pp20) REVERT: D 19 LYS cc_start: 0.8877 (tttt) cc_final: 0.8674 (tttm) REVERT: D 38 ARG cc_start: 0.7661 (ptm160) cc_final: 0.7184 (ttp-170) REVERT: E 33 VAL cc_start: 0.8233 (p) cc_final: 0.6967 (p) REVERT: E 66 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8360 (tttp) REVERT: E 97 LEU cc_start: 0.8553 (tp) cc_final: 0.8228 (tp) REVERT: E 106 VAL cc_start: 0.6327 (m) cc_final: 0.6016 (m) REVERT: F 616 ASN cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: F 640 GLN cc_start: 0.8997 (mm110) cc_final: 0.8758 (mm-40) REVERT: G 104 MET cc_start: 0.8905 (tpp) cc_final: 0.8265 (tpp) REVERT: G 129 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8341 (pp) REVERT: G 180 ASP cc_start: 0.9203 (m-30) cc_final: 0.8585 (m-30) REVERT: G 189 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8024 (mmmt) REVERT: G 308 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8099 (ttm170) REVERT: G 356 ASN cc_start: 0.9092 (t0) cc_final: 0.8678 (t0) REVERT: G 427 TRP cc_start: 0.8377 (m-90) cc_final: 0.7590 (m-90) REVERT: G 466 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: H 72 ASP cc_start: 0.8941 (t0) cc_final: 0.8599 (t0) REVERT: H 75 LYS cc_start: 0.8589 (pttt) cc_final: 0.8160 (pttm) REVERT: H 99 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8548 (tp40) REVERT: I 104 MET cc_start: 0.9048 (tpp) cc_final: 0.8698 (tpp) REVERT: I 150 MET cc_start: 0.9364 (mmm) cc_final: 0.9048 (mmm) REVERT: I 466 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: J 19 LYS cc_start: 0.8954 (tttt) cc_final: 0.8642 (tttm) REVERT: J 67 PHE cc_start: 0.6524 (m-80) cc_final: 0.6013 (m-80) REVERT: K 33 VAL cc_start: 0.8233 (p) cc_final: 0.7623 (p) REVERT: L 33 VAL cc_start: 0.7953 (p) cc_final: 0.6594 (p) REVERT: L 60 ASP cc_start: 0.8750 (p0) cc_final: 0.8511 (t0) REVERT: L 66 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8436 (ttpp) outliers start: 61 outliers final: 18 residues processed: 610 average time/residue: 0.1432 time to fit residues: 132.6225 Evaluate side-chains 418 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 394 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 313 PRO Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain J residue 83 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 300 ASN B 330 HIS B 428 GLN C 543 ASN C 575 GLN C 591 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 76 ASN D 81 GLN D 99 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN G 300 ASN G 330 HIS G 440 GLN H 81 GLN H 99 GLN I 258 GLN I 300 ASN I 330 HIS J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108580 restraints weight = 32376.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111989 restraints weight = 17711.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114297 restraints weight = 12143.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115792 restraints weight = 9496.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116697 restraints weight = 8077.840| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20613 Z= 0.158 Angle : 0.933 19.368 28152 Z= 0.434 Chirality : 0.055 0.612 3375 Planarity : 0.005 0.050 3432 Dihedral : 8.930 86.587 2632 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.15 % Favored : 88.68 % Rotamer: Outliers : 2.73 % Allowed : 11.18 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.83 (0.14), residues: 2367 helix: -3.79 (0.18), residues: 354 sheet: -2.76 (0.18), residues: 591 loop : -3.38 (0.13), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 151 TYR 0.014 0.001 TYR J 100E PHE 0.036 0.002 PHE J 100C TRP 0.025 0.002 TRP G 69 HIS 0.006 0.001 HIS K 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (20481) covalent geometry : angle 0.87387 / 0.42 (27798) SS BOND : bond 0.00446 / 0.28 ( 33) SS BOND : angle 0.74802 / 0.56 ( 66) hydrogen bonds : bond 0.05665 / 3.78 ( 367) hydrogen bonds : angle 7.23845 / 5.09 ( 936) Misc. bond : bond 0.00047 / 0.02 ( 3) link_ALPHA1-2 : bond 0.01401 / 0.66 ( 6) link_ALPHA1-2 : angle 2.72307 / 1.92 ( 18) link_ALPHA1-3 : bond 0.00065 / 0.03 ( 3) link_ALPHA1-3 : angle 3.15009 / 1.81 ( 9) link_ALPHA1-6 : bond 0.00545 / 0.25 ( 3) link_ALPHA1-6 : angle 1.42153 / 0.69 ( 9) link_BETA1-4 : bond 0.00989 / 0.58 ( 36) link_BETA1-4 : angle 2.86942 / 1.81 ( 108) link_NAG-ASN : bond 0.00687 / 0.46 ( 48) link_NAG-ASN : angle 3.84000 / 2.69 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 473 time to evaluate : 0.805 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: A 601 LYS cc_start: 0.9036 (mttp) cc_final: 0.8719 (mtmm) REVERT: B 95 MET cc_start: 0.8727 (ptm) cc_final: 0.8182 (ptt) REVERT: B 114 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 134 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.4730 (m-10) REVERT: B 154 LEU cc_start: 0.8322 (mt) cc_final: 0.7825 (mm) REVERT: B 432 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8034 (mm-40) REVERT: C 635 ILE cc_start: 0.8938 (tt) cc_final: 0.8559 (tt) REVERT: D 18 LEU cc_start: 0.8813 (tp) cc_final: 0.8570 (tp) REVERT: D 38 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7130 (ttp-170) REVERT: D 82 MET cc_start: 0.7603 (mmt) cc_final: 0.7265 (mmp) REVERT: E 66 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8189 (tttm) REVERT: F 616 ASN cc_start: 0.9293 (t0) cc_final: 0.9090 (t0) REVERT: F 635 ILE cc_start: 0.8931 (tt) cc_final: 0.8680 (tt) REVERT: G 104 MET cc_start: 0.8965 (tpp) cc_final: 0.8541 (tpp) REVERT: G 129 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8543 (pp) REVERT: G 180 ASP cc_start: 0.9039 (m-30) cc_final: 0.8440 (m-30) REVERT: G 308 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: G 356 ASN cc_start: 0.8974 (t0) cc_final: 0.8756 (t0) REVERT: G 432 GLN cc_start: 0.8732 (tp-100) cc_final: 0.8196 (mp10) REVERT: G 475 MET cc_start: 0.8507 (tpp) cc_final: 0.8264 (tpp) REVERT: H 72 ASP cc_start: 0.8849 (t0) cc_final: 0.8449 (t0) REVERT: H 75 LYS cc_start: 0.8506 (pttt) cc_final: 0.8157 (ptmt) REVERT: H 83 ARG cc_start: 0.7532 (pmt170) cc_final: 0.6710 (ptm160) REVERT: I 46 LYS cc_start: 0.5043 (mttm) cc_final: 0.4301 (mmtm) REVERT: I 104 MET cc_start: 0.9110 (tpp) cc_final: 0.8416 (tpp) REVERT: I 432 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8198 (mm110) REVERT: I 475 MET cc_start: 0.8665 (tpp) cc_final: 0.8384 (tpp) REVERT: J 19 LYS cc_start: 0.8925 (tttt) cc_final: 0.8660 (tttm) REVERT: J 83 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6720 (ttm-80) REVERT: J 97 TRP cc_start: 0.8954 (m100) cc_final: 0.8542 (m100) REVERT: K 18 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7994 (t) REVERT: L 31 GLU cc_start: 0.7854 (tp30) cc_final: 0.7298 (tp30) REVERT: L 33 VAL cc_start: 0.8004 (p) cc_final: 0.6576 (p) outliers start: 57 outliers final: 33 residues processed: 502 average time/residue: 0.1179 time to fit residues: 95.0297 Evaluate side-chains 429 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 390 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 36 optimal weight: 0.0980 chunk 231 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** 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 = 0.3593 r_free = 0.3593 target = 0.135907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108607 restraints weight = 32591.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112009 restraints weight = 17897.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114263 restraints weight = 12280.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115771 restraints weight = 9625.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116694 restraints weight = 8178.694| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20613 Z= 0.141 Angle : 0.849 17.991 28152 Z= 0.395 Chirality : 0.052 0.437 3375 Planarity : 0.004 0.044 3432 Dihedral : 7.843 78.024 2609 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.36 % Favored : 88.47 % Rotamer: Outliers : 2.88 % Allowed : 14.48 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.38 (0.15), residues: 2367 helix: -3.12 (0.21), residues: 354 sheet: -2.40 (0.20), residues: 597 loop : -3.22 (0.14), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.014 0.001 TYR K 49 PHE 0.031 0.002 PHE D 100C TRP 0.030 0.001 TRP G 69 HIS 0.002 0.001 HIS L 95B Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (20481) covalent geometry : angle 0.80614 / 0.39 (27798) SS BOND : bond 0.00675 / 0.44 ( 33) SS BOND : angle 0.65461 / 0.44 ( 66) hydrogen bonds : bond 0.04077 / 2.72 ( 367) hydrogen bonds : angle 6.31624 / 4.43 ( 936) Misc. bond : bond 0.00031 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01237 / 0.58 ( 6) link_ALPHA1-2 : angle 2.69090 / 1.87 ( 18) link_ALPHA1-3 : bond 0.00137 / 0.06 ( 3) link_ALPHA1-3 : angle 2.56436 / 1.45 ( 9) link_ALPHA1-6 : bond 0.00526 / 0.24 ( 3) link_ALPHA1-6 : angle 1.45676 / 0.74 ( 9) link_BETA1-4 : bond 0.00837 / 0.49 ( 36) link_BETA1-4 : angle 2.60950 / 1.64 ( 108) link_NAG-ASN : bond 0.00594 / 0.40 ( 48) link_NAG-ASN : angle 2.94884 / 2.04 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 418 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9154 (mttp) cc_final: 0.8876 (mtmm) REVERT: B 114 GLN cc_start: 0.8581 (tm130) cc_final: 0.8314 (tm-30) REVERT: B 134 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.4470 (m-10) REVERT: B 154 LEU cc_start: 0.8286 (mt) cc_final: 0.8028 (mm) REVERT: B 356 ASN cc_start: 0.8880 (t0) cc_final: 0.8641 (t0) REVERT: B 432 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8074 (mm-40) REVERT: C 571 TRP cc_start: 0.8320 (m100) cc_final: 0.8021 (m100) REVERT: C 635 ILE cc_start: 0.8865 (tt) cc_final: 0.8583 (tt) REVERT: C 650 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6345 (mm-40) REVERT: D 13 GLN cc_start: 0.8029 (mp10) cc_final: 0.7718 (mp10) REVERT: D 34 MET cc_start: 0.8992 (mmm) cc_final: 0.8777 (mmm) REVERT: D 38 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7263 (ttp-170) REVERT: D 67 PHE cc_start: 0.6545 (m-80) cc_final: 0.5929 (m-10) REVERT: D 82 MET cc_start: 0.7327 (mmt) cc_final: 0.7049 (mmt) REVERT: D 99 GLN cc_start: 0.8838 (tp40) cc_final: 0.8436 (tp-100) REVERT: E 66 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8131 (tttm) REVERT: F 635 ILE cc_start: 0.8825 (tt) cc_final: 0.8546 (tt) REVERT: G 129 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8687 (pp) REVERT: G 180 ASP cc_start: 0.8979 (m-30) cc_final: 0.8483 (m-30) REVERT: G 265 LEU cc_start: 0.9063 (mm) cc_final: 0.8774 (mt) REVERT: G 308 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7920 (mtt90) REVERT: G 356 ASN cc_start: 0.8989 (t0) cc_final: 0.8765 (t0) REVERT: G 427 TRP cc_start: 0.8183 (m-90) cc_final: 0.7651 (m-90) REVERT: G 432 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8174 (mp10) REVERT: H 72 ASP cc_start: 0.8779 (t0) cc_final: 0.8433 (t0) REVERT: H 82 MET cc_start: 0.7368 (mmp) cc_final: 0.6970 (mmp) REVERT: H 83 ARG cc_start: 0.7470 (pmt170) cc_final: 0.6997 (ttm-80) REVERT: H 99 GLN cc_start: 0.8597 (tp40) cc_final: 0.8106 (tp40) REVERT: I 46 LYS cc_start: 0.4961 (mttm) cc_final: 0.4312 (mmtp) REVERT: I 104 MET cc_start: 0.9104 (tpp) cc_final: 0.8615 (tpp) REVERT: I 150 MET cc_start: 0.9201 (mmm) cc_final: 0.8547 (mpp) REVERT: I 432 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8145 (mm110) REVERT: J 82 MET cc_start: 0.7236 (mmp) cc_final: 0.7000 (mmp) REVERT: J 83 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6918 (ttm-80) REVERT: J 97 TRP cc_start: 0.8927 (m100) cc_final: 0.8559 (m100) REVERT: J 99 GLN cc_start: 0.8575 (tp40) cc_final: 0.8324 (tp-100) REVERT: J 105 GLN cc_start: 0.8232 (pm20) cc_final: 0.7994 (pm20) REVERT: K 97 LEU cc_start: 0.8635 (tp) cc_final: 0.8200 (tt) REVERT: L 6 GLN cc_start: 0.7425 (pm20) cc_final: 0.7193 (pm20) REVERT: L 31 GLU cc_start: 0.7680 (tp30) cc_final: 0.7303 (tp30) REVERT: L 66 LYS cc_start: 0.8702 (ttpp) cc_final: 0.7924 (tttp) outliers start: 60 outliers final: 38 residues processed: 449 average time/residue: 0.1286 time to fit residues: 90.9809 Evaluate side-chains 430 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 388 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 83 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 167 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 133 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 640 GLN G 149 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109382 restraints weight = 32640.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112814 restraints weight = 18022.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115094 restraints weight = 12344.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116628 restraints weight = 9660.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117583 restraints weight = 8202.043| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20613 Z= 0.130 Angle : 0.800 17.396 28152 Z= 0.373 Chirality : 0.051 0.438 3375 Planarity : 0.004 0.051 3432 Dihedral : 7.248 59.977 2604 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 2.83 % Allowed : 15.97 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.97 (0.15), residues: 2367 helix: -2.37 (0.27), residues: 306 sheet: -2.15 (0.21), residues: 585 loop : -3.05 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.018 0.001 TYR B 134 PHE 0.032 0.002 PHE H 100C TRP 0.025 0.001 TRP B 69 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (20481) covalent geometry : angle 0.76091 / 0.36 (27798) SS BOND : bond 0.00247 / 0.15 ( 33) SS BOND : angle 0.52653 / 0.38 ( 66) hydrogen bonds : bond 0.03410 / 2.27 ( 367) hydrogen bonds : angle 5.81105 / 4.07 ( 936) Misc. bond : bond 0.00023 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01338 / 0.63 ( 6) link_ALPHA1-2 : angle 2.59710 / 1.81 ( 18) link_ALPHA1-3 : bond 0.00206 / 0.09 ( 3) link_ALPHA1-3 : angle 2.24047 / 1.26 ( 9) link_ALPHA1-6 : bond 0.00532 / 0.25 ( 3) link_ALPHA1-6 : angle 1.42353 / 0.73 ( 9) link_BETA1-4 : bond 0.00783 / 0.46 ( 36) link_BETA1-4 : angle 2.39503 / 1.50 ( 108) link_NAG-ASN : bond 0.00555 / 0.39 ( 48) link_NAG-ASN : angle 2.74241 / 1.92 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 409 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9062 (mttp) cc_final: 0.8642 (mtmm) REVERT: B 103 GLN cc_start: 0.7970 (pt0) cc_final: 0.7614 (tt0) REVERT: B 114 GLN cc_start: 0.8562 (tm130) cc_final: 0.8320 (tm-30) REVERT: B 134 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.4527 (m-80) REVERT: B 154 LEU cc_start: 0.8271 (mt) cc_final: 0.8035 (mm) REVERT: B 432 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8060 (mm-40) REVERT: C 635 ILE cc_start: 0.8834 (tt) cc_final: 0.8549 (tt) REVERT: C 650 GLN cc_start: 0.7153 (mm-40) cc_final: 0.6611 (mm-40) REVERT: D 13 GLN cc_start: 0.7967 (mp10) cc_final: 0.7613 (mp10) REVERT: D 34 MET cc_start: 0.8682 (mmm) cc_final: 0.8432 (mmm) REVERT: D 72 ASP cc_start: 0.8801 (t0) cc_final: 0.8495 (t0) REVERT: D 83 ARG cc_start: 0.7345 (pmt-80) cc_final: 0.6802 (mtp85) REVERT: D 99 GLN cc_start: 0.8664 (tp40) cc_final: 0.8274 (tp-100) REVERT: E 66 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8368 (tttp) REVERT: F 635 ILE cc_start: 0.8774 (tt) cc_final: 0.8506 (tt) REVERT: G 129 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8370 (pp) REVERT: G 180 ASP cc_start: 0.9062 (m-30) cc_final: 0.8561 (m-30) REVERT: G 265 LEU cc_start: 0.9074 (mm) cc_final: 0.8749 (mt) REVERT: G 308 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7976 (mtt90) REVERT: G 356 ASN cc_start: 0.8994 (t0) cc_final: 0.8765 (t0) REVERT: G 427 TRP cc_start: 0.8109 (m-90) cc_final: 0.7492 (m-90) REVERT: G 432 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8151 (mp10) REVERT: H 72 ASP cc_start: 0.8770 (t0) cc_final: 0.8467 (t0) REVERT: H 83 ARG cc_start: 0.7448 (pmt170) cc_final: 0.6755 (ptm160) REVERT: H 99 GLN cc_start: 0.8528 (tp40) cc_final: 0.8037 (tp40) REVERT: I 46 LYS cc_start: 0.4804 (mttm) cc_final: 0.4194 (mmtp) REVERT: I 104 MET cc_start: 0.9075 (tpp) cc_final: 0.8714 (tpp) REVERT: I 432 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8202 (mm110) REVERT: J 83 ARG cc_start: 0.7497 (pmt-80) cc_final: 0.7061 (ttm-80) REVERT: J 97 TRP cc_start: 0.8915 (m100) cc_final: 0.8541 (m100) REVERT: J 105 GLN cc_start: 0.8091 (pm20) cc_final: 0.7771 (pm20) REVERT: K 38 GLN cc_start: 0.7722 (tt0) cc_final: 0.7440 (tt0) REVERT: L 31 GLU cc_start: 0.7810 (tp30) cc_final: 0.7550 (tp30) REVERT: L 66 LYS cc_start: 0.8657 (ttpp) cc_final: 0.7999 (tttp) outliers start: 59 outliers final: 41 residues processed: 444 average time/residue: 0.1258 time to fit residues: 88.9542 Evaluate side-chains 439 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 395 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 664 ASP Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 119 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN G 258 GLN G 478 ASN H 81 GLN J 99 GLN ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107824 restraints weight = 32340.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111202 restraints weight = 17912.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113446 restraints weight = 12303.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114934 restraints weight = 9653.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.115894 restraints weight = 8211.293| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20613 Z= 0.144 Angle : 0.795 17.099 28152 Z= 0.369 Chirality : 0.051 0.434 3375 Planarity : 0.004 0.042 3432 Dihedral : 6.880 57.836 2589 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.94 % Favored : 88.89 % Rotamer: Outliers : 3.93 % Allowed : 16.26 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.76 (0.15), residues: 2367 helix: -1.95 (0.28), residues: 318 sheet: -2.00 (0.21), residues: 579 loop : -2.98 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 71 TYR 0.020 0.001 TYR B 134 PHE 0.031 0.002 PHE H 102 TRP 0.026 0.001 TRP G 69 HIS 0.002 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (20481) covalent geometry : angle 0.75709 / 0.36 (27798) SS BOND : bond 0.00414 / 0.27 ( 33) SS BOND : angle 0.60747 / 0.42 ( 66) hydrogen bonds : bond 0.03473 / 2.33 ( 367) hydrogen bonds : angle 5.62577 / 3.94 ( 936) Misc. bond : bond 0.00025 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01313 / 0.60 ( 6) link_ALPHA1-2 : angle 2.69411 / 1.87 ( 18) link_ALPHA1-3 : bond 0.00190 / 0.09 ( 3) link_ALPHA1-3 : angle 2.18057 / 1.21 ( 9) link_ALPHA1-6 : bond 0.00494 / 0.23 ( 3) link_ALPHA1-6 : angle 1.44779 / 0.74 ( 9) link_BETA1-4 : bond 0.00764 / 0.45 ( 36) link_BETA1-4 : angle 2.31356 / 1.45 ( 108) link_NAG-ASN : bond 0.00574 / 0.40 ( 48) link_NAG-ASN : angle 2.72369 / 1.90 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 409 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.9013 (mttp) cc_final: 0.8561 (mtmm) REVERT: B 103 GLN cc_start: 0.8188 (pt0) cc_final: 0.7883 (tt0) REVERT: B 114 GLN cc_start: 0.8587 (tm130) cc_final: 0.8322 (tm-30) REVERT: B 134 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.4758 (m-80) REVERT: B 432 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8083 (mm-40) REVERT: C 635 ILE cc_start: 0.8935 (tt) cc_final: 0.8580 (tt) REVERT: C 650 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6745 (mm-40) REVERT: D 72 ASP cc_start: 0.8827 (t0) cc_final: 0.8511 (t0) REVERT: D 82 MET cc_start: 0.8414 (mmt) cc_final: 0.8206 (mmp) REVERT: D 83 ARG cc_start: 0.7425 (pmt-80) cc_final: 0.7185 (pmt-80) REVERT: D 99 GLN cc_start: 0.8582 (tp40) cc_final: 0.8180 (tp-100) REVERT: E 66 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8376 (tttp) REVERT: E 89 GLN cc_start: 0.8365 (pp30) cc_final: 0.8155 (pp30) REVERT: F 635 ILE cc_start: 0.8913 (tt) cc_final: 0.8709 (tt) REVERT: G 80 ASN cc_start: 0.8355 (m-40) cc_final: 0.8058 (p0) REVERT: G 129 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8356 (pp) REVERT: G 134 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: G 180 ASP cc_start: 0.9055 (m-30) cc_final: 0.8528 (m-30) REVERT: G 308 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: G 356 ASN cc_start: 0.9000 (t0) cc_final: 0.8730 (t0) REVERT: G 427 TRP cc_start: 0.8114 (m-90) cc_final: 0.7504 (m-90) REVERT: G 432 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8151 (mp10) REVERT: H 72 ASP cc_start: 0.8782 (t0) cc_final: 0.8470 (t0) REVERT: H 82 MET cc_start: 0.7377 (mmt) cc_final: 0.7089 (mmp) REVERT: H 83 ARG cc_start: 0.7454 (pmt170) cc_final: 0.6784 (ptm160) REVERT: I 46 LYS cc_start: 0.4852 (mttm) cc_final: 0.4255 (mmtp) REVERT: I 432 GLN cc_start: 0.8582 (tp-100) cc_final: 0.8029 (mp10) REVERT: J 72 ASP cc_start: 0.8927 (t0) cc_final: 0.8647 (t0) REVERT: J 83 ARG cc_start: 0.7242 (pmt-80) cc_final: 0.7003 (ttm170) REVERT: J 97 TRP cc_start: 0.8865 (m100) cc_final: 0.8598 (m100) REVERT: J 105 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: K 20 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7320 (mmt-90) REVERT: K 38 GLN cc_start: 0.7834 (tt0) cc_final: 0.7458 (tt0) REVERT: K 97 LEU cc_start: 0.8844 (tp) cc_final: 0.8578 (tt) REVERT: L 66 LYS cc_start: 0.8658 (ttpp) cc_final: 0.7991 (tttp) REVERT: L 79 GLU cc_start: 0.7548 (tp30) cc_final: 0.7020 (mp0) outliers start: 82 outliers final: 60 residues processed: 458 average time/residue: 0.1274 time to fit residues: 93.5153 Evaluate side-chains 461 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 396 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 326 ILE Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 177 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 160 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** I 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 GLN ** 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 = 0.3585 r_free = 0.3585 target = 0.135481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107699 restraints weight = 32400.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111045 restraints weight = 18137.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113311 restraints weight = 12588.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114811 restraints weight = 9900.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115704 restraints weight = 8453.511| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20613 Z= 0.137 Angle : 0.779 16.377 28152 Z= 0.363 Chirality : 0.050 0.433 3375 Planarity : 0.004 0.054 3432 Dihedral : 6.545 57.427 2583 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 3.60 % Allowed : 17.36 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.74 (0.16), residues: 2367 helix: -1.96 (0.27), residues: 336 sheet: -1.96 (0.20), residues: 621 loop : -3.00 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.018 0.001 TYR B 134 PHE 0.026 0.002 PHE D 100C TRP 0.027 0.001 TRP B 69 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (20481) covalent geometry : angle 0.74252 / 0.36 (27798) SS BOND : bond 0.00284 / 0.18 ( 33) SS BOND : angle 0.59691 / 0.41 ( 66) hydrogen bonds : bond 0.03309 / 2.22 ( 367) hydrogen bonds : angle 5.46373 / 3.83 ( 936) Misc. bond : bond 0.00028 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01271 / 0.58 ( 6) link_ALPHA1-2 : angle 2.63526 / 1.82 ( 18) link_ALPHA1-3 : bond 0.00221 / 0.11 ( 3) link_ALPHA1-3 : angle 2.11760 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00536 / 0.25 ( 3) link_ALPHA1-6 : angle 1.47327 / 0.75 ( 9) link_BETA1-4 : bond 0.00753 / 0.44 ( 36) link_BETA1-4 : angle 2.22706 / 1.39 ( 108) link_NAG-ASN : bond 0.00568 / 0.40 ( 48) link_NAG-ASN : angle 2.68090 / 1.87 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 400 time to evaluate : 0.730 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: A 601 LYS cc_start: 0.8969 (mttp) cc_final: 0.8550 (mtmm) REVERT: A 660 LEU cc_start: 0.8996 (mt) cc_final: 0.8775 (mt) REVERT: B 46 LYS cc_start: 0.6024 (mmtm) cc_final: 0.5615 (mmtm) REVERT: B 103 GLN cc_start: 0.8290 (pt0) cc_final: 0.7865 (tt0) REVERT: B 114 GLN cc_start: 0.8542 (tm130) cc_final: 0.8194 (tm-30) REVERT: B 134 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.4872 (m-80) REVERT: B 432 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8093 (mm-40) REVERT: C 635 ILE cc_start: 0.8912 (tt) cc_final: 0.8643 (tt) REVERT: C 650 GLN cc_start: 0.7142 (mm-40) cc_final: 0.6776 (mm-40) REVERT: D 72 ASP cc_start: 0.8803 (t0) cc_final: 0.8519 (t0) REVERT: D 82 MET cc_start: 0.8356 (mmt) cc_final: 0.8133 (mmp) REVERT: D 99 GLN cc_start: 0.8569 (tp40) cc_final: 0.8138 (tp-100) REVERT: E 66 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8239 (tttp) REVERT: F 635 ILE cc_start: 0.8833 (tt) cc_final: 0.8600 (tt) REVERT: G 80 ASN cc_start: 0.8408 (m-40) cc_final: 0.8123 (p0) REVERT: G 129 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8379 (pp) REVERT: G 134 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.5592 (m-80) REVERT: G 180 ASP cc_start: 0.9065 (m-30) cc_final: 0.8558 (m-30) REVERT: G 308 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7830 (mtt90) REVERT: G 356 ASN cc_start: 0.9070 (t0) cc_final: 0.8800 (t0) REVERT: G 427 TRP cc_start: 0.8089 (m-90) cc_final: 0.7485 (m-90) REVERT: G 432 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8147 (mp10) REVERT: H 72 ASP cc_start: 0.8786 (t0) cc_final: 0.8470 (t0) REVERT: H 83 ARG cc_start: 0.7413 (pmt170) cc_final: 0.6697 (ptm160) REVERT: I 46 LYS cc_start: 0.4806 (mttm) cc_final: 0.4371 (mmtp) REVERT: I 432 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8026 (mp10) REVERT: J 72 ASP cc_start: 0.8859 (t0) cc_final: 0.8564 (t0) REVERT: J 83 ARG cc_start: 0.7254 (pmt-80) cc_final: 0.6941 (ttm170) REVERT: J 97 TRP cc_start: 0.8914 (m100) cc_final: 0.8661 (m100) REVERT: J 105 GLN cc_start: 0.8220 (pm20) cc_final: 0.7739 (pm20) REVERT: K 20 ARG cc_start: 0.7783 (mmt90) cc_final: 0.7416 (mmt90) REVERT: K 38 GLN cc_start: 0.7834 (tt0) cc_final: 0.7492 (tt0) REVERT: K 97 LEU cc_start: 0.8842 (tp) cc_final: 0.8584 (tt) REVERT: L 31 GLU cc_start: 0.8175 (tp30) cc_final: 0.7614 (tp30) REVERT: L 33 VAL cc_start: 0.7690 (p) cc_final: 0.6776 (p) REVERT: L 66 LYS cc_start: 0.8677 (ttpp) cc_final: 0.7886 (tttm) REVERT: L 79 GLU cc_start: 0.7582 (tp30) cc_final: 0.7001 (mp0) outliers start: 75 outliers final: 56 residues processed: 450 average time/residue: 0.1220 time to fit residues: 87.7494 Evaluate side-chains 450 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 390 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 308 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 446 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 419 ARG Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 105 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 193 optimal weight: 0.0050 chunk 139 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 156 optimal weight: 0.0010 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 119 optimal weight: 0.0370 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** K 34 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.138216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110842 restraints weight = 32161.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114268 restraints weight = 17766.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116553 restraints weight = 12199.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118073 restraints weight = 9552.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118983 restraints weight = 8110.368| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20613 Z= 0.114 Angle : 0.751 16.027 28152 Z= 0.350 Chirality : 0.049 0.421 3375 Planarity : 0.004 0.045 3432 Dihedral : 6.086 49.976 2578 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 3.07 % Allowed : 17.84 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -3.54 (0.16), residues: 2367 helix: -1.73 (0.28), residues: 324 sheet: -1.90 (0.21), residues: 615 loop : -2.84 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 71 TYR 0.016 0.001 TYR B 134 PHE 0.026 0.001 PHE D 100C TRP 0.031 0.001 TRP B 69 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (20481) covalent geometry : angle 0.71659 / 0.34 (27798) SS BOND : bond 0.00202 / 0.13 ( 33) SS BOND : angle 0.43626 / 0.30 ( 66) hydrogen bonds : bond 0.02820 / 1.88 ( 367) hydrogen bonds : angle 5.22612 / 3.68 ( 936) Misc. bond : bond 0.00008 / 0.00 ( 3) link_ALPHA1-2 : bond 0.01299 / 0.59 ( 6) link_ALPHA1-2 : angle 2.55567 / 1.76 ( 18) link_ALPHA1-3 : bond 0.00309 / 0.14 ( 3) link_ALPHA1-3 : angle 1.92873 / 1.08 ( 9) link_ALPHA1-6 : bond 0.00609 / 0.28 ( 3) link_ALPHA1-6 : angle 1.46478 / 0.75 ( 9) link_BETA1-4 : bond 0.00728 / 0.43 ( 36) link_BETA1-4 : angle 2.08978 / 1.31 ( 108) link_NAG-ASN : bond 0.00569 / 0.40 ( 48) link_NAG-ASN : angle 2.55182 / 1.79 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 428 time to evaluate : 0.627 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 601 LYS cc_start: 0.8868 (mttp) cc_final: 0.8485 (mtmm) REVERT: B 46 LYS cc_start: 0.5764 (mmtm) cc_final: 0.5385 (mmtp) REVERT: B 103 GLN cc_start: 0.8209 (pt0) cc_final: 0.7847 (tt0) REVERT: B 134 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5043 (m-10) REVERT: B 432 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8066 (mm-40) REVERT: C 635 ILE cc_start: 0.8761 (tt) cc_final: 0.8512 (tt) REVERT: C 650 GLN cc_start: 0.7000 (mm-40) cc_final: 0.6522 (mm-40) REVERT: D 72 ASP cc_start: 0.8798 (t0) cc_final: 0.8530 (t0) REVERT: D 83 ARG cc_start: 0.6475 (pmt170) cc_final: 0.6174 (pmt-80) REVERT: D 99 GLN cc_start: 0.8341 (tp40) cc_final: 0.7948 (tp-100) REVERT: E 66 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8199 (tttp) REVERT: F 635 ILE cc_start: 0.8760 (tt) cc_final: 0.8542 (tt) REVERT: G 80 ASN cc_start: 0.8472 (m-40) cc_final: 0.8184 (p0) REVERT: G 129 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8301 (pp) REVERT: G 134 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: G 180 ASP cc_start: 0.9058 (m-30) cc_final: 0.8597 (m-30) REVERT: G 356 ASN cc_start: 0.9043 (t0) cc_final: 0.8774 (t0) REVERT: G 432 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8122 (mp10) REVERT: H 13 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: H 72 ASP cc_start: 0.8781 (t0) cc_final: 0.8466 (t0) REVERT: H 82 MET cc_start: 0.8400 (mmt) cc_final: 0.8019 (mmp) REVERT: H 83 ARG cc_start: 0.7444 (pmt170) cc_final: 0.7053 (ttm-80) REVERT: I 69 TRP cc_start: 0.6277 (p-90) cc_final: 0.5934 (p-90) REVERT: I 80 ASN cc_start: 0.8709 (m-40) cc_final: 0.8116 (p0) REVERT: I 111 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8870 (tt) REVERT: I 432 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8015 (mp10) REVERT: J 72 ASP cc_start: 0.8806 (t0) cc_final: 0.8513 (t0) REVERT: J 97 TRP cc_start: 0.8803 (m100) cc_final: 0.8588 (m100) REVERT: K 20 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7451 (mmt90) REVERT: K 38 GLN cc_start: 0.7804 (tt0) cc_final: 0.7446 (tt0) REVERT: K 97 LEU cc_start: 0.8773 (tp) cc_final: 0.8496 (tt) REVERT: L 31 GLU cc_start: 0.7991 (tp30) cc_final: 0.7457 (tp30) REVERT: L 33 VAL cc_start: 0.8153 (p) cc_final: 0.6951 (p) REVERT: L 66 LYS cc_start: 0.8671 (ttpp) cc_final: 0.7956 (tttp) outliers start: 64 outliers final: 44 residues processed: 467 average time/residue: 0.1306 time to fit residues: 97.1528 Evaluate side-chains 447 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 398 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 34 GLN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 0.1980 chunk 182 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 GLN H 99 GLN I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.135800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108014 restraints weight = 32239.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111372 restraints weight = 17857.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113632 restraints weight = 12360.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115127 restraints weight = 9737.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116033 restraints weight = 8304.244| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20613 Z= 0.121 Angle : 0.748 15.983 28152 Z= 0.348 Chirality : 0.049 0.418 3375 Planarity : 0.004 0.047 3432 Dihedral : 5.894 48.386 2574 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.35 % Favored : 89.48 % Rotamer: Outliers : 3.65 % Allowed : 18.37 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.43 (0.16), residues: 2367 helix: -1.53 (0.29), residues: 327 sheet: -1.84 (0.21), residues: 612 loop : -2.78 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.018 0.001 TYR B 134 PHE 0.023 0.001 PHE D 67 TRP 0.032 0.001 TRP B 69 HIS 0.002 0.000 HIS B 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (20481) covalent geometry : angle 0.71472 / 0.34 (27798) SS BOND : bond 0.00223 / 0.14 ( 33) SS BOND : angle 0.57601 / 0.36 ( 66) hydrogen bonds : bond 0.02907 / 1.94 ( 367) hydrogen bonds : angle 5.11777 / 3.61 ( 936) Misc. bond : bond 0.00013 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01312 / 0.60 ( 6) link_ALPHA1-2 : angle 2.60037 / 1.79 ( 18) link_ALPHA1-3 : bond 0.00247 / 0.12 ( 3) link_ALPHA1-3 : angle 1.88815 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00575 / 0.27 ( 3) link_ALPHA1-6 : angle 1.46243 / 0.75 ( 9) link_BETA1-4 : bond 0.00714 / 0.42 ( 36) link_BETA1-4 : angle 2.04013 / 1.28 ( 108) link_NAG-ASN : bond 0.00559 / 0.39 ( 48) link_NAG-ASN : angle 2.51396 / 1.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 402 time to evaluate : 0.700 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: A 601 LYS cc_start: 0.8822 (mttp) cc_final: 0.8444 (mtmm) REVERT: B 46 LYS cc_start: 0.5848 (mmtm) cc_final: 0.5456 (mmtp) REVERT: B 103 GLN cc_start: 0.8301 (pt0) cc_final: 0.7968 (tt0) REVERT: B 134 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5466 (m-80) REVERT: B 150 MET cc_start: 0.9186 (tpp) cc_final: 0.8845 (mmt) REVERT: B 432 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8067 (mm-40) REVERT: C 635 ILE cc_start: 0.8767 (tt) cc_final: 0.8505 (tt) REVERT: C 650 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6687 (mm-40) REVERT: D 18 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8499 (mt) REVERT: D 28 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8428 (p) REVERT: D 34 MET cc_start: 0.8709 (mmm) cc_final: 0.8378 (mmm) REVERT: D 72 ASP cc_start: 0.8855 (t0) cc_final: 0.8535 (t0) REVERT: D 99 GLN cc_start: 0.8289 (tp40) cc_final: 0.8018 (tp-100) REVERT: E 66 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8195 (tttp) REVERT: F 635 ILE cc_start: 0.8778 (tt) cc_final: 0.8508 (tt) REVERT: G 80 ASN cc_start: 0.8528 (m-40) cc_final: 0.8191 (p0) REVERT: G 129 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8276 (pp) REVERT: G 134 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: G 180 ASP cc_start: 0.9066 (m-30) cc_final: 0.8581 (m-30) REVERT: G 356 ASN cc_start: 0.9033 (t0) cc_final: 0.8737 (t0) REVERT: G 426 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7214 (ptm) REVERT: G 427 TRP cc_start: 0.8090 (m-90) cc_final: 0.7184 (m-90) REVERT: G 432 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8133 (mp10) REVERT: H 28 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8699 (p) REVERT: H 72 ASP cc_start: 0.8791 (t0) cc_final: 0.8470 (t0) REVERT: H 82 MET cc_start: 0.8423 (mmt) cc_final: 0.7988 (mmp) REVERT: I 69 TRP cc_start: 0.6242 (p-90) cc_final: 0.5940 (p-90) REVERT: I 80 ASN cc_start: 0.8761 (m-40) cc_final: 0.8125 (p0) REVERT: I 111 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8962 (tt) REVERT: I 432 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8013 (mp10) REVERT: J 72 ASP cc_start: 0.8842 (t0) cc_final: 0.8586 (t0) REVERT: J 83 ARG cc_start: 0.6827 (pmt-80) cc_final: 0.6429 (ttm170) REVERT: K 38 GLN cc_start: 0.7795 (tt0) cc_final: 0.7447 (tt0) REVERT: K 97 LEU cc_start: 0.8746 (tp) cc_final: 0.8465 (tt) REVERT: L 31 GLU cc_start: 0.7960 (tp30) cc_final: 0.7519 (tp30) REVERT: L 66 LYS cc_start: 0.8667 (ttpp) cc_final: 0.7872 (tttp) outliers start: 76 outliers final: 57 residues processed: 447 average time/residue: 0.1286 time to fit residues: 92.3123 Evaluate side-chains 453 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 388 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 137 ASN Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 83 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 142 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 203 optimal weight: 50.0000 chunk 3 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN I 137 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108038 restraints weight = 32203.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111435 restraints weight = 17959.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113720 restraints weight = 12429.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115099 restraints weight = 9781.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116151 restraints weight = 8385.620| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20613 Z= 0.121 Angle : 0.752 15.512 28152 Z= 0.351 Chirality : 0.049 0.416 3375 Planarity : 0.004 0.042 3432 Dihedral : 5.831 48.025 2574 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.98 % Favored : 88.85 % Rotamer: Outliers : 3.50 % Allowed : 18.80 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.35 (0.16), residues: 2367 helix: -1.49 (0.28), residues: 339 sheet: -1.71 (0.21), residues: 591 loop : -2.77 (0.14), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 71 TYR 0.018 0.001 TYR B 134 PHE 0.020 0.001 PHE D 100C TRP 0.033 0.001 TRP B 69 HIS 0.004 0.001 HIS C 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20481) covalent geometry : angle 0.71938 / 0.34 (27798) SS BOND : bond 0.00200 / 0.13 ( 33) SS BOND : angle 0.91500 / 0.62 ( 66) hydrogen bonds : bond 0.02865 / 1.90 ( 367) hydrogen bonds : angle 5.06863 / 3.59 ( 936) Misc. bond : bond 0.00012 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01329 / 0.61 ( 6) link_ALPHA1-2 : angle 2.56308 / 1.77 ( 18) link_ALPHA1-3 : bond 0.00257 / 0.12 ( 3) link_ALPHA1-3 : angle 1.84875 / 1.03 ( 9) link_ALPHA1-6 : bond 0.00585 / 0.27 ( 3) link_ALPHA1-6 : angle 1.48593 / 0.76 ( 9) link_BETA1-4 : bond 0.00704 / 0.41 ( 36) link_BETA1-4 : angle 1.99788 / 1.25 ( 108) link_NAG-ASN : bond 0.00560 / 0.39 ( 48) link_NAG-ASN : angle 2.48563 / 1.74 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 397 time to evaluate : 0.545 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: A 601 LYS cc_start: 0.8757 (mttp) cc_final: 0.8390 (mtmm) REVERT: B 46 LYS cc_start: 0.5878 (mmtm) cc_final: 0.5588 (mmtp) REVERT: B 103 GLN cc_start: 0.8316 (pt0) cc_final: 0.7988 (tt0) REVERT: B 134 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: B 150 MET cc_start: 0.9129 (tpp) cc_final: 0.8817 (mmt) REVERT: B 432 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8088 (mm-40) REVERT: C 635 ILE cc_start: 0.8765 (tt) cc_final: 0.8514 (tt) REVERT: C 650 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6686 (mm-40) REVERT: D 18 LEU cc_start: 0.8693 (mt) cc_final: 0.8476 (mt) REVERT: D 28 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (p) REVERT: D 34 MET cc_start: 0.8709 (mmm) cc_final: 0.8357 (mmm) REVERT: D 72 ASP cc_start: 0.8873 (t0) cc_final: 0.8639 (t0) REVERT: D 99 GLN cc_start: 0.8400 (tp40) cc_final: 0.7982 (tp-100) REVERT: E 66 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8179 (tttp) REVERT: F 635 ILE cc_start: 0.8793 (tt) cc_final: 0.8532 (tt) REVERT: G 80 ASN cc_start: 0.8626 (m-40) cc_final: 0.8272 (p0) REVERT: G 129 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8349 (pp) REVERT: G 134 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: G 180 ASP cc_start: 0.9081 (m-30) cc_final: 0.8587 (m-30) REVERT: G 356 ASN cc_start: 0.9021 (t0) cc_final: 0.8724 (t0) REVERT: G 426 MET cc_start: 0.7727 (ptm) cc_final: 0.7211 (ptm) REVERT: G 427 TRP cc_start: 0.7965 (m-90) cc_final: 0.7061 (m-90) REVERT: G 432 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8131 (mp10) REVERT: H 28 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8527 (p) REVERT: H 34 MET cc_start: 0.8767 (mmm) cc_final: 0.8551 (mmm) REVERT: H 47 TRP cc_start: 0.8742 (t60) cc_final: 0.8127 (t60) REVERT: H 72 ASP cc_start: 0.8807 (t0) cc_final: 0.8481 (t0) REVERT: I 69 TRP cc_start: 0.6214 (p-90) cc_final: 0.5944 (p-90) REVERT: I 80 ASN cc_start: 0.8734 (m-40) cc_final: 0.8127 (p0) REVERT: I 111 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8981 (tt) REVERT: I 432 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8015 (mp10) REVERT: J 72 ASP cc_start: 0.8855 (t0) cc_final: 0.8579 (t0) REVERT: J 83 ARG cc_start: 0.6796 (pmt-80) cc_final: 0.6468 (ttm170) REVERT: K 38 GLN cc_start: 0.7791 (tt0) cc_final: 0.7434 (tt0) REVERT: K 97 LEU cc_start: 0.8736 (tp) cc_final: 0.8469 (tt) REVERT: L 31 GLU cc_start: 0.7893 (tp30) cc_final: 0.7482 (tp30) REVERT: L 66 LYS cc_start: 0.8745 (ttpp) cc_final: 0.7898 (tttp) outliers start: 73 outliers final: 59 residues processed: 441 average time/residue: 0.1254 time to fit residues: 88.8723 Evaluate side-chains 445 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 380 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 93 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 221 optimal weight: 0.0020 chunk 231 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 HIS A 577 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.136171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108196 restraints weight = 32418.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111613 restraints weight = 18017.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.113907 restraints weight = 12452.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115295 restraints weight = 9789.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116341 restraints weight = 8392.529| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20613 Z= 0.121 Angle : 0.749 15.175 28152 Z= 0.350 Chirality : 0.049 0.412 3375 Planarity : 0.004 0.045 3432 Dihedral : 5.749 47.432 2574 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.73 % Favored : 89.10 % Rotamer: Outliers : 3.26 % Allowed : 19.18 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.30 (0.16), residues: 2367 helix: -1.37 (0.29), residues: 339 sheet: -1.60 (0.22), residues: 558 loop : -2.77 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.019 0.001 TYR B 134 PHE 0.019 0.001 PHE D 100C TRP 0.035 0.001 TRP B 69 HIS 0.010 0.001 HIS C 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20481) covalent geometry : angle 0.71776 / 0.34 (27798) SS BOND : bond 0.00209 / 0.13 ( 33) SS BOND : angle 0.81290 / 0.56 ( 66) hydrogen bonds : bond 0.02866 / 1.91 ( 367) hydrogen bonds : angle 5.02849 / 3.57 ( 936) Misc. bond : bond 0.00012 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01241 / 0.56 ( 6) link_ALPHA1-2 : angle 2.54102 / 1.74 ( 18) link_ALPHA1-3 : bond 0.00251 / 0.12 ( 3) link_ALPHA1-3 : angle 1.81209 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00583 / 0.27 ( 3) link_ALPHA1-6 : angle 1.49723 / 0.76 ( 9) link_BETA1-4 : bond 0.00689 / 0.40 ( 36) link_BETA1-4 : angle 1.95395 / 1.22 ( 108) link_NAG-ASN : bond 0.00557 / 0.39 ( 48) link_NAG-ASN : angle 2.45679 / 1.72 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 397 time to evaluate : 0.745 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: A 601 LYS cc_start: 0.8719 (mttp) cc_final: 0.8367 (mtmm) REVERT: A 625 ASN cc_start: 0.8886 (m-40) cc_final: 0.8658 (m-40) REVERT: B 46 LYS cc_start: 0.5869 (mmtm) cc_final: 0.5445 (mmtp) REVERT: B 134 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: B 150 MET cc_start: 0.9085 (tpp) cc_final: 0.8789 (mmt) REVERT: B 432 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8120 (mm-40) REVERT: C 635 ILE cc_start: 0.8747 (tt) cc_final: 0.8496 (tt) REVERT: C 650 GLN cc_start: 0.6994 (mm-40) cc_final: 0.6743 (mm-40) REVERT: D 28 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8403 (p) REVERT: D 34 MET cc_start: 0.8715 (mmm) cc_final: 0.8387 (mmm) REVERT: D 72 ASP cc_start: 0.8871 (t0) cc_final: 0.8558 (t0) REVERT: D 99 GLN cc_start: 0.8346 (tp40) cc_final: 0.7931 (tp-100) REVERT: E 66 LYS cc_start: 0.8796 (ttpt) cc_final: 0.7997 (tttp) REVERT: F 635 ILE cc_start: 0.8779 (tt) cc_final: 0.8539 (tt) REVERT: G 80 ASN cc_start: 0.8655 (m-40) cc_final: 0.8275 (p0) REVERT: G 129 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8327 (pp) REVERT: G 134 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: G 180 ASP cc_start: 0.9088 (m-30) cc_final: 0.8595 (m-30) REVERT: G 217 TYR cc_start: 0.8783 (m-10) cc_final: 0.8545 (m-80) REVERT: G 356 ASN cc_start: 0.9020 (t0) cc_final: 0.8711 (t0) REVERT: G 426 MET cc_start: 0.7613 (ptm) cc_final: 0.7181 (ptm) REVERT: G 427 TRP cc_start: 0.7964 (m-90) cc_final: 0.7116 (m-90) REVERT: G 432 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8110 (mp10) REVERT: H 28 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8509 (p) REVERT: H 34 MET cc_start: 0.8765 (mmm) cc_final: 0.8505 (mmm) REVERT: H 47 TRP cc_start: 0.8754 (t60) cc_final: 0.8192 (t60) REVERT: H 72 ASP cc_start: 0.8830 (t0) cc_final: 0.8494 (t0) REVERT: I 111 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8995 (tt) REVERT: I 432 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8014 (mp10) REVERT: J 72 ASP cc_start: 0.8911 (t0) cc_final: 0.8656 (t0) REVERT: J 97 TRP cc_start: 0.8679 (m100) cc_final: 0.8272 (m100) REVERT: K 38 GLN cc_start: 0.7773 (tt0) cc_final: 0.7454 (tt0) REVERT: K 97 LEU cc_start: 0.8637 (tp) cc_final: 0.8412 (tt) REVERT: L 31 GLU cc_start: 0.7882 (tp30) cc_final: 0.7402 (tp30) REVERT: L 66 LYS cc_start: 0.8753 (ttpp) cc_final: 0.7950 (tttp) REVERT: L 82 ASP cc_start: 0.7658 (p0) cc_final: 0.7433 (p0) REVERT: L 89 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8007 (tm-30) outliers start: 68 outliers final: 57 residues processed: 439 average time/residue: 0.1286 time to fit residues: 91.0844 Evaluate side-chains 454 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 391 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 419 ARG Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 134 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 370 GLU Chi-restraints excluded: chain I residue 424 ILE Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 170 optimal weight: 0.0270 chunk 113 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS G 478 ASN ** I 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108240 restraints weight = 32504.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111613 restraints weight = 18256.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113865 restraints weight = 12669.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115230 restraints weight = 9995.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116327 restraints weight = 8585.658| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 20613 Z= 0.151 Angle : 0.880 59.197 28152 Z= 0.452 Chirality : 0.050 0.415 3375 Planarity : 0.004 0.081 3432 Dihedral : 5.768 47.392 2574 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.69 % Favored : 89.14 % Rotamer: Outliers : 3.17 % Allowed : 19.52 % Favored : 77.31 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.30 (0.16), residues: 2367 helix: -1.40 (0.29), residues: 339 sheet: -1.59 (0.22), residues: 558 loop : -2.77 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG J 66 TYR 0.019 0.001 TYR B 134 PHE 0.024 0.001 PHE J 67 TRP 0.032 0.001 TRP B 69 HIS 0.009 0.001 HIS C 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (20481) covalent geometry : angle 0.85467 / 0.45 (27798) SS BOND : bond 0.00463 / 0.24 ( 33) SS BOND : angle 1.02074 / 0.81 ( 66) hydrogen bonds : bond 0.02939 / 1.94 ( 367) hydrogen bonds : angle 5.04039 / 3.57 ( 936) Misc. bond : bond 0.00012 / 0.01 ( 3) link_ALPHA1-2 : bond 0.01270 / 0.56 ( 6) link_ALPHA1-2 : angle 2.55014 / 1.75 ( 18) link_ALPHA1-3 : bond 0.00243 / 0.11 ( 3) link_ALPHA1-3 : angle 1.80419 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00582 / 0.27 ( 3) link_ALPHA1-6 : angle 1.49594 / 0.76 ( 9) link_BETA1-4 : bond 0.00680 / 0.40 ( 36) link_BETA1-4 : angle 1.94964 / 1.22 ( 108) link_NAG-ASN : bond 0.00559 / 0.39 ( 48) link_NAG-ASN : angle 2.45784 / 1.72 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3077.78 seconds wall clock time: 54 minutes 4.38 seconds (3244.38 seconds total)