Starting phenix.real_space_refine on Sun Jul 5 03:55:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.map" model { file = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8epn_28531/07_2026/8epn_28531.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 99 5.16 5 C 15915 2.51 5 N 3993 2.21 5 O 5070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25077 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 49, 'TRANS': 943} Chain breaks: 9 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.48, per 1000 atoms: 0.22 Number of scatterers: 25077 At special positions: 0 Unit cell: (145.39, 143.38, 175.54, 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 99 16.00 O 5070 8.00 N 3993 7.00 C 15915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 5 " " BMA d 3 " - " MAN d 5 " " BMA h 3 " - " MAN h 5 " BETA1-4 " 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 H 2 " - " BMA H 3 " " 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 L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1201 " - " ASN A 709 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 234 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B 603 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 234 " " NAG C1201 " - " ASN C 709 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 234 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 282 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A 657 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN B 616 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B 657 " " NAG U 1 " - " ASN B 122 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C 657 " " NAG f 1 " - " ASN C 122 " " NAG g 1 " - " ASN C1098 " " NAG h 1 " - " ASN C1134 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C 331 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 624.3 milliseconds 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 43 sheets defined 26.5% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.108A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.967A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.518A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.518A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.540A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.530A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.290A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.076A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.295A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.113A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.525A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.641A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.511A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.512A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.514A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.296A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.072A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.302A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.163A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.654A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.517A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.542A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.303A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.074A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.301A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 5.841A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.114A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.725A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.813A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.938A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.120A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.270A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.968A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.926A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.730A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.753A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.607A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.118A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.048A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.581A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.786A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.249A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.907A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.691A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.678A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.869A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.077A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.008A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.816A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.272A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1082 1007 hydrogen bonds defined for protein. 2757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7757 1.34 - 1.46: 6330 1.46 - 1.58: 11395 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 25605 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" N THR C 393 " pdb=" CA THR C 393 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 7.16e+00 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.89e+00 ... (remaining 25600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 34064 2.33 - 4.67: 648 4.67 - 7.00: 108 7.00 - 9.33: 1 9.33 - 11.66: 3 Bond angle restraints: 34824 Sorted by residual: angle pdb=" C ASN A1135 " pdb=" N THR A1136 " pdb=" CA THR A1136 " ideal model delta sigma weight residual 121.70 133.36 -11.66 1.80e+00 3.09e-01 4.20e+01 angle pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta sigma weight residual 121.70 133.32 -11.62 1.80e+00 3.09e-01 4.17e+01 angle pdb=" C ASN B1135 " pdb=" N THR B1136 " pdb=" CA THR B1136 " ideal model delta sigma weight residual 121.70 133.30 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 117.23 111.18 6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 111.20 6.03 1.36e+00 5.41e-01 1.97e+01 ... (remaining 34819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12912 17.98 - 35.95: 1045 35.95 - 53.93: 227 53.93 - 71.90: 60 71.90 - 89.88: 33 Dihedral angle restraints: 14277 sinusoidal: 5562 harmonic: 8715 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -163.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.99 75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -161.95 75.95 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 14274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3685 0.072 - 0.144: 611 0.144 - 0.215: 12 0.215 - 0.287: 13 0.287 - 0.359: 14 Chirality restraints: 4335 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 4332 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B1132 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE B1132 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C1132 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ILE C1132 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C1132 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C1133 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO A 139 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2685 2.75 - 3.29: 23064 3.29 - 3.83: 39662 3.83 - 4.36: 45309 4.36 - 4.90: 79566 Nonbonded interactions: 190286 Sorted by model distance: nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS C 825 " pdb=" O THR C 941 " model vdw 2.269 3.120 ... (remaining 190281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.400 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.500 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 25758 Z= 0.238 Angle : 0.790 11.663 35256 Z= 0.363 Chirality : 0.053 0.359 4335 Planarity : 0.004 0.043 4314 Dihedral : 14.564 89.877 8574 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.84 % Allowed : 12.38 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 2931 helix: 1.64 (0.21), residues: 669 sheet: 0.67 (0.21), residues: 543 loop : -1.06 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 457 TYR 0.021 0.001 TYR A 453 PHE 0.018 0.001 PHE A 140 TRP 0.012 0.002 TRP C 353 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 (25605) covalent geometry : angle 0.75109 / 0.35 (34824) SS BOND : bond 0.00275 / 0.17 ( 27) SS BOND : angle 1.05999 / 0.71 ( 54) hydrogen bonds : bond 0.21895 / 14.19 ( 1001) hydrogen bonds : angle 8.34392 / 5.67 ( 2757) link_ALPHA1-3 : bond 0.00427 / 0.25 ( 15) link_ALPHA1-3 : angle 1.75971 / 1.12 ( 45) link_ALPHA1-6 : bond 0.00614 / 0.38 ( 15) link_ALPHA1-6 : angle 1.58007 / 1.02 ( 45) link_BETA1-4 : bond 0.00545 / 0.34 ( 48) link_BETA1-4 : angle 2.03902 / 1.32 ( 144) link_NAG-ASN : bond 0.00438 / 0.28 ( 48) link_NAG-ASN : angle 3.14943 / 2.06 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7629 (m-80) cc_final: 0.7120 (m-80) REVERT: C 133 PHE cc_start: 0.7579 (m-80) cc_final: 0.7088 (m-80) outliers start: 22 outliers final: 19 residues processed: 116 average time/residue: 0.4400 time to fit residues: 62.6974 Evaluate side-chains 93 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 657 ASN Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.119246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.072677 restraints weight = 60332.416| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.23 r_work: 0.2982 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25758 Z= 0.220 Angle : 0.672 9.003 35256 Z= 0.336 Chirality : 0.048 0.353 4335 Planarity : 0.005 0.048 4314 Dihedral : 5.014 45.941 3230 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.11 % Allowed : 11.57 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 2931 helix: 1.72 (0.21), residues: 690 sheet: 0.70 (0.21), residues: 543 loop : -1.22 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 646 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.002 PHE B 135 TRP 0.011 0.002 TRP C 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (25605) covalent geometry : angle 0.63618 / 0.33 (34824) SS BOND : bond 0.00520 / 0.29 ( 27) SS BOND : angle 0.85662 / 0.53 ( 54) hydrogen bonds : bond 0.08418 / 5.54 ( 1001) hydrogen bonds : angle 6.51246 / 4.45 ( 2757) link_ALPHA1-3 : bond 0.00645 / 0.38 ( 15) link_ALPHA1-3 : angle 1.48752 / 0.96 ( 45) link_ALPHA1-6 : bond 0.00731 / 0.46 ( 15) link_ALPHA1-6 : angle 1.77124 / 1.14 ( 45) link_BETA1-4 : bond 0.00408 / 0.27 ( 48) link_BETA1-4 : angle 1.76784 / 1.18 ( 144) link_NAG-ASN : bond 0.00489 / 0.30 ( 48) link_NAG-ASN : angle 2.78322 / 1.89 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 80 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: B 133 PHE cc_start: 0.7755 (m-80) cc_final: 0.7186 (m-80) REVERT: C 133 PHE cc_start: 0.7660 (m-80) cc_final: 0.7106 (m-80) outliers start: 55 outliers final: 18 residues processed: 129 average time/residue: 0.3874 time to fit residues: 63.1857 Evaluate side-chains 85 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 181 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 chunk 67 optimal weight: 0.0050 chunk 248 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 240 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.120813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075401 restraints weight = 60906.638| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.12 r_work: 0.3045 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25758 Z= 0.120 Angle : 0.568 9.421 35256 Z= 0.279 Chirality : 0.045 0.345 4335 Planarity : 0.004 0.042 4314 Dihedral : 4.512 45.180 3211 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.22 % Allowed : 11.34 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.15), residues: 2931 helix: 2.09 (0.21), residues: 684 sheet: 0.83 (0.22), residues: 534 loop : -1.13 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.021 0.001 TYR A 453 PHE 0.013 0.001 PHE A 400 TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (25605) covalent geometry : angle 0.53037 / 0.27 (34824) SS BOND : bond 0.00231 / 0.16 ( 27) SS BOND : angle 0.83334 / 0.55 ( 54) hydrogen bonds : bond 0.06286 / 4.12 ( 1001) hydrogen bonds : angle 5.84009 / 3.96 ( 2757) link_ALPHA1-3 : bond 0.00630 / 0.37 ( 15) link_ALPHA1-3 : angle 1.41598 / 0.92 ( 45) link_ALPHA1-6 : bond 0.00721 / 0.44 ( 15) link_ALPHA1-6 : angle 1.55612 / 1.01 ( 45) link_BETA1-4 : bond 0.00497 / 0.32 ( 48) link_BETA1-4 : angle 1.58445 / 1.05 ( 144) link_NAG-ASN : bond 0.00496 / 0.30 ( 48) link_NAG-ASN : angle 2.61432 / 1.79 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 85 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 TYR cc_start: 0.8241 (m-80) cc_final: 0.7980 (m-10) REVERT: B 133 PHE cc_start: 0.7695 (m-80) cc_final: 0.7096 (m-80) REVERT: B 957 GLN cc_start: 0.8753 (tt0) cc_final: 0.8523 (tt0) REVERT: C 133 PHE cc_start: 0.7661 (m-80) cc_final: 0.7095 (m-80) REVERT: C 239 GLN cc_start: 0.7137 (tp-100) cc_final: 0.6742 (mm-40) outliers start: 58 outliers final: 26 residues processed: 139 average time/residue: 0.3988 time to fit residues: 68.2683 Evaluate side-chains 96 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 105 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.120113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074019 restraints weight = 60514.931| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.13 r_work: 0.2993 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25758 Z= 0.184 Angle : 0.615 9.604 35256 Z= 0.301 Chirality : 0.047 0.342 4335 Planarity : 0.004 0.044 4314 Dihedral : 4.457 43.846 3205 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 11.72 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2931 helix: 2.05 (0.21), residues: 687 sheet: 0.77 (0.21), residues: 576 loop : -1.12 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.019 0.001 TYR C1067 PHE 0.014 0.001 PHE B 238 TRP 0.008 0.002 TRP B 436 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (25605) covalent geometry : angle 0.57984 / 0.29 (34824) SS BOND : bond 0.00349 / 0.22 ( 27) SS BOND : angle 0.69200 / 0.45 ( 54) hydrogen bonds : bond 0.07457 / 4.93 ( 1001) hydrogen bonds : angle 5.82990 / 3.96 ( 2757) link_ALPHA1-3 : bond 0.00628 / 0.36 ( 15) link_ALPHA1-3 : angle 1.43438 / 0.94 ( 45) link_ALPHA1-6 : bond 0.00688 / 0.41 ( 15) link_ALPHA1-6 : angle 1.66974 / 1.08 ( 45) link_BETA1-4 : bond 0.00431 / 0.28 ( 48) link_BETA1-4 : angle 1.58309 / 1.04 ( 144) link_NAG-ASN : bond 0.00434 / 0.27 ( 48) link_NAG-ASN : angle 2.66748 / 1.85 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 79 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7710 (tmmt) REVERT: A 227 VAL cc_start: 0.8804 (t) cc_final: 0.8545 (p) REVERT: B 133 PHE cc_start: 0.7833 (m-80) cc_final: 0.7232 (m-80) REVERT: B 227 VAL cc_start: 0.8845 (t) cc_final: 0.8539 (p) REVERT: C 133 PHE cc_start: 0.7662 (m-80) cc_final: 0.7149 (m-80) REVERT: C 239 GLN cc_start: 0.7324 (tp-100) cc_final: 0.6808 (mm-40) REVERT: C 380 TYR cc_start: 0.6011 (m-10) cc_final: 0.5731 (m-10) REVERT: C 740 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8345 (tpt) REVERT: C 1144 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 63 outliers final: 34 residues processed: 137 average time/residue: 0.4062 time to fit residues: 69.3511 Evaluate side-chains 110 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 5 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073987 restraints weight = 60676.396| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.16 r_work: 0.3013 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25758 Z= 0.153 Angle : 0.591 9.566 35256 Z= 0.288 Chirality : 0.046 0.338 4335 Planarity : 0.004 0.044 4314 Dihedral : 4.457 48.824 3205 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.15 % Allowed : 12.03 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 2931 helix: 2.14 (0.21), residues: 684 sheet: 0.97 (0.22), residues: 543 loop : -1.08 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.022 0.001 TYR A 707 PHE 0.018 0.001 PHE B 400 TRP 0.031 0.002 TRP B 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25605) covalent geometry : angle 0.55438 / 0.28 (34824) SS BOND : bond 0.00285 / 0.17 ( 27) SS BOND : angle 0.93199 / 0.57 ( 54) hydrogen bonds : bond 0.06862 / 4.52 ( 1001) hydrogen bonds : angle 5.63286 / 3.82 ( 2757) link_ALPHA1-3 : bond 0.00614 / 0.36 ( 15) link_ALPHA1-3 : angle 1.41668 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00730 / 0.45 ( 15) link_ALPHA1-6 : angle 1.63436 / 1.06 ( 45) link_BETA1-4 : bond 0.00453 / 0.29 ( 48) link_BETA1-4 : angle 1.55528 / 1.03 ( 144) link_NAG-ASN : bond 0.00444 / 0.27 ( 48) link_NAG-ASN : angle 2.64351 / 1.84 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 80 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7717 (tmmt) REVERT: A 227 VAL cc_start: 0.8829 (t) cc_final: 0.8569 (p) REVERT: B 133 PHE cc_start: 0.7814 (m-80) cc_final: 0.7258 (m-80) REVERT: B 190 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7273 (ttm170) REVERT: B 227 VAL cc_start: 0.8844 (t) cc_final: 0.8542 (p) REVERT: B 794 ILE cc_start: 0.7550 (pt) cc_final: 0.7341 (mm) REVERT: C 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.7175 (m-80) REVERT: C 314 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8246 (tp40) REVERT: C 380 TYR cc_start: 0.6102 (m-10) cc_final: 0.5882 (m-10) REVERT: C 740 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8331 (tpt) REVERT: C 1144 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7728 (mm-30) outliers start: 56 outliers final: 36 residues processed: 131 average time/residue: 0.4491 time to fit residues: 72.7778 Evaluate side-chains 113 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 237 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 259 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.121044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074903 restraints weight = 60272.545| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 4.24 r_work: 0.3027 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25758 Z= 0.125 Angle : 0.564 9.565 35256 Z= 0.272 Chirality : 0.045 0.329 4335 Planarity : 0.004 0.062 4314 Dihedral : 4.332 50.423 3205 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.18 % Allowed : 12.41 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2931 helix: 2.21 (0.21), residues: 684 sheet: 1.05 (0.23), residues: 525 loop : -1.03 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.016 0.001 TYR A1067 PHE 0.019 0.001 PHE C 400 TRP 0.012 0.001 TRP B 353 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (25605) covalent geometry : angle 0.52716 / 0.26 (34824) SS BOND : bond 0.00277 / 0.18 ( 27) SS BOND : angle 0.71003 / 0.47 ( 54) hydrogen bonds : bond 0.06327 / 4.17 ( 1001) hydrogen bonds : angle 5.50834 / 3.73 ( 2757) link_ALPHA1-3 : bond 0.00602 / 0.35 ( 15) link_ALPHA1-3 : angle 1.41985 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00730 / 0.45 ( 15) link_ALPHA1-6 : angle 1.60571 / 1.04 ( 45) link_BETA1-4 : bond 0.00451 / 0.29 ( 48) link_BETA1-4 : angle 1.51870 / 1.00 ( 144) link_NAG-ASN : bond 0.00439 / 0.27 ( 48) link_NAG-ASN : angle 2.57142 / 1.79 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7774 (tmmt) REVERT: A 227 VAL cc_start: 0.8822 (t) cc_final: 0.8562 (p) REVERT: A 314 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: B 133 PHE cc_start: 0.7785 (m-80) cc_final: 0.7193 (m-80) REVERT: B 227 VAL cc_start: 0.8847 (t) cc_final: 0.8564 (p) REVERT: B 794 ILE cc_start: 0.7507 (pt) cc_final: 0.7295 (mm) REVERT: B 957 GLN cc_start: 0.8814 (tt0) cc_final: 0.8591 (tt0) REVERT: C 133 PHE cc_start: 0.7631 (m-80) cc_final: 0.7147 (m-80) REVERT: C 227 VAL cc_start: 0.8829 (t) cc_final: 0.8574 (p) REVERT: C 239 GLN cc_start: 0.7173 (tp40) cc_final: 0.6725 (mm-40) REVERT: C 314 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8218 (tp40) REVERT: C 740 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8321 (tpt) REVERT: C 1144 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7735 (mm-30) outliers start: 57 outliers final: 42 residues processed: 139 average time/residue: 0.4212 time to fit residues: 73.2295 Evaluate side-chains 122 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 76 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 259 optimal weight: 0.0030 chunk 174 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 162 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.121282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075855 restraints weight = 60395.862| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.07 r_work: 0.3046 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25758 Z= 0.114 Angle : 0.553 9.550 35256 Z= 0.266 Chirality : 0.045 0.328 4335 Planarity : 0.004 0.057 4314 Dihedral : 4.251 51.500 3205 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 12.80 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 2931 helix: 2.28 (0.21), residues: 684 sheet: 0.89 (0.22), residues: 555 loop : -1.01 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.016 0.001 TYR A1067 PHE 0.017 0.001 PHE B 541 TRP 0.034 0.001 TRP B 353 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (25605) covalent geometry : angle 0.51745 / 0.26 (34824) SS BOND : bond 0.00290 / 0.19 ( 27) SS BOND : angle 0.59213 / 0.41 ( 54) hydrogen bonds : bond 0.05962 / 3.93 ( 1001) hydrogen bonds : angle 5.40703 / 3.66 ( 2757) link_ALPHA1-3 : bond 0.00594 / 0.35 ( 15) link_ALPHA1-3 : angle 1.41632 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00725 / 0.46 ( 15) link_ALPHA1-6 : angle 1.57801 / 1.03 ( 45) link_BETA1-4 : bond 0.00451 / 0.29 ( 48) link_BETA1-4 : angle 1.49316 / 0.98 ( 144) link_NAG-ASN : bond 0.00440 / 0.27 ( 48) link_NAG-ASN : angle 2.53635 / 1.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 90 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7716 (tmmt) REVERT: A 227 VAL cc_start: 0.8828 (t) cc_final: 0.8568 (p) REVERT: A 314 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8287 (tp40) REVERT: A 386 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7451 (mttt) REVERT: B 133 PHE cc_start: 0.7753 (m-80) cc_final: 0.7160 (m-80) REVERT: B 227 VAL cc_start: 0.8837 (t) cc_final: 0.8561 (p) REVERT: B 541 PHE cc_start: 0.5719 (m-10) cc_final: 0.4444 (m-10) REVERT: B 957 GLN cc_start: 0.8790 (tt0) cc_final: 0.8570 (tt0) REVERT: C 133 PHE cc_start: 0.7637 (m-80) cc_final: 0.7150 (m-80) REVERT: C 227 VAL cc_start: 0.8822 (t) cc_final: 0.8572 (p) REVERT: C 239 GLN cc_start: 0.7188 (tp40) cc_final: 0.6635 (mm-40) REVERT: C 314 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8225 (tp40) REVERT: C 386 LYS cc_start: 0.7578 (mttt) cc_final: 0.7318 (mttt) REVERT: C 740 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8303 (tpt) REVERT: C 1144 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7757 (mm-30) outliers start: 53 outliers final: 42 residues processed: 137 average time/residue: 0.4401 time to fit residues: 75.1689 Evaluate side-chains 123 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 77 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 294 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.0170 chunk 186 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.122078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077092 restraints weight = 60638.682| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.14 r_work: 0.3078 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25758 Z= 0.102 Angle : 0.543 14.478 35256 Z= 0.259 Chirality : 0.044 0.323 4335 Planarity : 0.004 0.048 4314 Dihedral : 4.150 52.641 3205 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.11 % Allowed : 12.95 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2931 helix: 2.39 (0.21), residues: 684 sheet: 0.75 (0.21), residues: 591 loop : -0.89 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.020 0.001 TYR C 453 PHE 0.016 0.001 PHE C 400 TRP 0.024 0.001 TRP B 353 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 (25605) covalent geometry : angle 0.50817 / 0.25 (34824) SS BOND : bond 0.00253 / 0.16 ( 27) SS BOND : angle 0.53952 / 0.38 ( 54) hydrogen bonds : bond 0.05262 / 3.46 ( 1001) hydrogen bonds : angle 5.28635 / 3.57 ( 2757) link_ALPHA1-3 : bond 0.00587 / 0.35 ( 15) link_ALPHA1-3 : angle 1.40820 / 0.92 ( 45) link_ALPHA1-6 : bond 0.00716 / 0.43 ( 15) link_ALPHA1-6 : angle 1.52831 / 0.99 ( 45) link_BETA1-4 : bond 0.00466 / 0.30 ( 48) link_BETA1-4 : angle 1.45303 / 0.96 ( 144) link_NAG-ASN : bond 0.00457 / 0.28 ( 48) link_NAG-ASN : angle 2.47701 / 1.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 94 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7802 (tmmt) REVERT: A 227 VAL cc_start: 0.8811 (t) cc_final: 0.8561 (p) REVERT: A 314 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8283 (tp40) REVERT: A 386 LYS cc_start: 0.7611 (mtmt) cc_final: 0.7322 (mttt) REVERT: A 541 PHE cc_start: 0.5531 (m-10) cc_final: 0.4714 (m-10) REVERT: B 65 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: B 133 PHE cc_start: 0.7746 (m-80) cc_final: 0.7099 (m-80) REVERT: B 227 VAL cc_start: 0.8821 (t) cc_final: 0.8549 (p) REVERT: B 957 GLN cc_start: 0.8795 (tt0) cc_final: 0.8592 (tt0) REVERT: C 133 PHE cc_start: 0.7631 (m-80) cc_final: 0.7154 (m-80) REVERT: C 227 VAL cc_start: 0.8801 (t) cc_final: 0.8560 (p) REVERT: C 239 GLN cc_start: 0.7162 (tp40) cc_final: 0.6699 (mm-40) REVERT: C 314 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8187 (tp40) REVERT: C 541 PHE cc_start: 0.5498 (m-10) cc_final: 0.4741 (m-10) REVERT: C 740 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8254 (tpt) REVERT: C 1144 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7782 (mm-30) outliers start: 55 outliers final: 40 residues processed: 142 average time/residue: 0.4335 time to fit residues: 76.3569 Evaluate side-chains 121 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 76 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 81 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 259 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.119624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073073 restraints weight = 60165.094| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 4.19 r_work: 0.2971 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 25758 Z= 0.240 Angle : 0.666 9.674 35256 Z= 0.328 Chirality : 0.049 0.353 4335 Planarity : 0.005 0.053 4314 Dihedral : 4.635 50.265 3205 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.03 % Allowed : 13.14 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 2931 helix: 2.06 (0.21), residues: 684 sheet: 0.85 (0.22), residues: 555 loop : -1.04 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 454 TYR 0.025 0.002 TYR C 453 PHE 0.020 0.002 PHE B 318 TRP 0.015 0.002 TRP B 353 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (25605) covalent geometry : angle 0.63404 / 0.32 (34824) SS BOND : bond 0.00374 / 0.23 ( 27) SS BOND : angle 0.82099 / 0.54 ( 54) hydrogen bonds : bond 0.08234 / 5.45 ( 1001) hydrogen bonds : angle 5.79227 / 3.93 ( 2757) link_ALPHA1-3 : bond 0.00622 / 0.36 ( 15) link_ALPHA1-3 : angle 1.46130 / 0.97 ( 45) link_ALPHA1-6 : bond 0.00677 / 0.43 ( 15) link_ALPHA1-6 : angle 1.74818 / 1.11 ( 45) link_BETA1-4 : bond 0.00411 / 0.26 ( 48) link_BETA1-4 : angle 1.54512 / 1.01 ( 144) link_NAG-ASN : bond 0.00452 / 0.29 ( 48) link_NAG-ASN : angle 2.68143 / 1.86 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 85 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7756 (tmmt) REVERT: A 227 VAL cc_start: 0.8862 (t) cc_final: 0.8602 (p) REVERT: A 314 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8303 (tp40) REVERT: B 133 PHE cc_start: 0.7786 (m-80) cc_final: 0.7229 (m-80) REVERT: B 227 VAL cc_start: 0.8849 (t) cc_final: 0.8568 (p) REVERT: C 133 PHE cc_start: 0.7594 (m-80) cc_final: 0.7208 (m-80) REVERT: C 227 VAL cc_start: 0.8855 (t) cc_final: 0.8599 (p) REVERT: C 239 GLN cc_start: 0.7322 (tp40) cc_final: 0.6751 (mm-40) REVERT: C 380 TYR cc_start: 0.6339 (m-10) cc_final: 0.6133 (m-10) REVERT: C 386 LYS cc_start: 0.7511 (mttt) cc_final: 0.7286 (mttt) REVERT: C 1144 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7790 (mm-30) outliers start: 53 outliers final: 32 residues processed: 134 average time/residue: 0.3961 time to fit residues: 66.8794 Evaluate side-chains 110 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 157 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 257 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 236 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.121013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074951 restraints weight = 60351.388| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.20 r_work: 0.3022 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25758 Z= 0.130 Angle : 0.580 9.524 35256 Z= 0.281 Chirality : 0.045 0.322 4335 Planarity : 0.004 0.048 4314 Dihedral : 4.490 53.440 3205 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.19 % Allowed : 14.02 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 2931 helix: 2.35 (0.21), residues: 663 sheet: 0.98 (0.22), residues: 531 loop : -0.97 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.020 0.001 TYR C 453 PHE 0.021 0.001 PHE B 400 TRP 0.039 0.002 TRP B 353 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25605) covalent geometry : angle 0.54529 / 0.27 (34824) SS BOND : bond 0.00295 / 0.19 ( 27) SS BOND : angle 0.59951 / 0.42 ( 54) hydrogen bonds : bond 0.06516 / 4.29 ( 1001) hydrogen bonds : angle 5.56315 / 3.77 ( 2757) link_ALPHA1-3 : bond 0.00596 / 0.35 ( 15) link_ALPHA1-3 : angle 1.42538 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00757 / 0.48 ( 15) link_ALPHA1-6 : angle 1.59996 / 1.04 ( 45) link_BETA1-4 : bond 0.00465 / 0.30 ( 48) link_BETA1-4 : angle 1.53138 / 1.01 ( 144) link_NAG-ASN : bond 0.00435 / 0.27 ( 48) link_NAG-ASN : angle 2.54063 / 1.75 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5862 Ramachandran restraints generated. 2931 Oldfield, 0 Emsley, 2931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7779 (tmmt) REVERT: A 227 VAL cc_start: 0.8829 (t) cc_final: 0.8580 (p) REVERT: A 314 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8292 (tp40) REVERT: A 386 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7395 (mttt) REVERT: B 133 PHE cc_start: 0.7725 (m-80) cc_final: 0.7160 (m-80) REVERT: B 227 VAL cc_start: 0.8830 (t) cc_final: 0.8554 (p) REVERT: C 133 PHE cc_start: 0.7634 (m-80) cc_final: 0.7210 (m-80) REVERT: C 227 VAL cc_start: 0.8829 (t) cc_final: 0.8579 (p) REVERT: C 239 GLN cc_start: 0.7269 (tp40) cc_final: 0.6826 (mm110) REVERT: C 1144 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7802 (mm-30) outliers start: 31 outliers final: 27 residues processed: 111 average time/residue: 0.4579 time to fit residues: 62.3159 Evaluate side-chains 106 residues out of total 2610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 979 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 289 optimal weight: 4.9990 chunk 268 optimal weight: 0.0270 chunk 80 optimal weight: 4.9990 chunk 173 optimal weight: 0.0170 chunk 249 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 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 = 0.4105 r_free = 0.4105 target = 0.122126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.077021 restraints weight = 60509.250| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.12 r_work: 0.3068 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25758 Z= 0.104 Angle : 0.550 9.516 35256 Z= 0.265 Chirality : 0.044 0.320 4335 Planarity : 0.004 0.044 4314 Dihedral : 4.270 54.530 3205 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.11 % Allowed : 14.33 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.43 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 2931 helix: 2.55 (0.21), residues: 663 sheet: 0.83 (0.21), residues: 561 loop : -0.90 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.021 0.001 TYR C 453 PHE 0.017 0.001 PHE B 541 TRP 0.055 0.002 TRP B 353 HIS 0.001 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (25605) covalent geometry : angle 0.51639 / 0.26 (34824) SS BOND : bond 0.00260 / 0.17 ( 27) SS BOND : angle 0.53619 / 0.39 ( 54) hydrogen bonds : bond 0.05271 / 3.46 ( 1001) hydrogen bonds : angle 5.32775 / 3.62 ( 2757) link_ALPHA1-3 : bond 0.00589 / 0.35 ( 15) link_ALPHA1-3 : angle 1.42069 / 0.93 ( 45) link_ALPHA1-6 : bond 0.00717 / 0.45 ( 15) link_ALPHA1-6 : angle 1.54115 / 1.00 ( 45) link_BETA1-4 : bond 0.00458 / 0.29 ( 48) link_BETA1-4 : angle 1.44628 / 0.95 ( 144) link_NAG-ASN : bond 0.00440 / 0.27 ( 48) link_NAG-ASN : angle 2.42696 / 1.66 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8432.34 seconds wall clock time: 144 minutes 39.00 seconds (8679.00 seconds total)