Starting phenix.real_space_refine on Thu Sep 18 16:58:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq1_25376/09_2025/7sq1_25376.map" } resolution = 3.8 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= 0.001 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 121 5.16 5 C 11459 2.51 5 N 3049 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18340 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3467 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3512 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3497 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18340 At special positions: 0 Unit cell: (189, 152.88, 123.48, 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 121 16.00 O 3711 8.00 N 3049 7.00 C 11459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS C 501 " distance=2.05 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.16 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.06 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.22 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.18 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.26 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.08 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.15 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.10 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.19 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.07 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM18122 C6 NAG E 608 45.489 78.875 67.940 1.00 90.40 C !!! !!! HETATM17308 C6 NAG V 1 46.816 79.842 68.554 1.00 85.00 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Atom "HETATM17708 O5 NAG h 2 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 1 " - " MAN O 2 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA O 1 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 462 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 398 " " NAG G 611 " - " ASN G 462 " " NAG J 1 " - " ASN C 133 " " NAG K 1 " - " ASN C 197 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 234 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN E 295 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 355 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 392 " " NAG b 1 " - " ASN E 398 " " NAG c 1 " - " ASN G 133 " " NAG d 1 " - " ASN G 156 " " NAG e 1 " - " ASN G 160 " " NAG f 1 " - " ASN G 234 " " NAG g 1 " - " ASN G 262 " " NAG h 1 " - " ASN G 355 " " NAG i 1 " - " ASN G 386 " " NAG j 1 " - " ASN G 448 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 817.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 42 sheets defined 24.5% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.234A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.629A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.941A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.801A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.611A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.800A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.544A pdb=" N HIS C 72 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.813A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.648A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.690A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.743A pdb=" N SER D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.634A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.701A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.858A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 4.092A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.692A pdb=" N HIS E 72 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.717A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.236A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.750A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.799A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.666A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.941A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.615A pdb=" N HIS G 72 " --> pdb=" O TRP G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.674A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.532A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.668A pdb=" N TYR A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 52A through 54 Processing helix chain 'A' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.546A pdb=" N CYS B 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR C 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL B 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.691A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.721A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.360A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 302 through 309 removed outlier: 4.730A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.301A pdb=" N CYS D 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.656A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.300A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.446A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 302 through 309 removed outlier: 4.736A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.686A pdb=" N MET L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.560A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.113A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.611A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.345A pdb=" N CYS F 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR G 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR F 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL G 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL F 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.675A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 133 removed outlier: 3.544A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.387A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.383A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 304 through 309 removed outlier: 3.555A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.146A pdb=" N PHE I 98 " --> pdb=" O GLN I 90 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLN I 90 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY I 100 " --> pdb=" O CYS I 88 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 88 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.100A pdb=" N MET A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.593A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3190 1.32 - 1.44: 5014 1.44 - 1.57: 10329 1.57 - 1.70: 2 1.70 - 1.82: 168 Bond restraints: 18703 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" C2 NAG B 701 " ideal model delta sigma weight residual 1.532 1.603 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.449 0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB TYR A 32 " pdb=" CG TYR A 32 " ideal model delta sigma weight residual 1.512 1.444 0.068 2.20e-02 2.07e+03 9.65e+00 bond pdb=" CG ASP H 101 " pdb=" OD1 ASP H 101 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.29e+00 bond pdb=" CB LEU C 111 " pdb=" CG LEU C 111 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 9.08e+00 ... (remaining 18698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.94: 25368 8.94 - 17.88: 9 17.88 - 26.82: 0 26.82 - 35.76: 0 35.76 - 44.70: 6 Bond angle restraints: 25383 Sorted by residual: angle pdb=" C8 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" N2 NAG G 610 " ideal model delta sigma weight residual 115.06 159.76 -44.70 3.00e+00 1.11e-01 2.22e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" N2 NAG F 701 " ideal model delta sigma weight residual 115.06 159.74 -44.68 3.00e+00 1.11e-01 2.22e+02 angle pdb=" N2 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" O7 NAG G 610 " ideal model delta sigma weight residual 123.46 80.00 43.46 3.00e+00 1.11e-01 2.10e+02 angle pdb=" N2 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 123.46 80.02 43.44 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 121.48 79.72 41.76 3.00e+00 1.11e-01 1.94e+02 ... (remaining 25378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 12100 21.90 - 43.79: 227 43.79 - 65.69: 93 65.69 - 87.59: 58 87.59 - 109.48: 21 Dihedral angle restraints: 12499 sinusoidal: 6289 harmonic: 6210 Sorted by residual: dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -137.19 51.19 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.23 42.23 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 12496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 3068 0.263 - 0.527: 29 0.527 - 0.790: 5 0.790 - 1.053: 1 1.053 - 1.317: 1 Chirality restraints: 3104 Sorted by residual: chirality pdb=" C1 MAN O 2 " pdb=" O3 BMA O 1 " pdb=" C2 MAN O 2 " pdb=" O5 MAN O 2 " both_signs ideal model delta sigma weight residual False 2.40 1.08 1.32 2.00e-02 2.50e+03 4.34e+03 chirality pdb=" C1 BMA O 1 " pdb=" O4 NAG N 2 " pdb=" C2 BMA O 1 " pdb=" O5 BMA O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-02 2.50e+03 1.40e+03 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.30e+02 ... (remaining 3101 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.094 2.00e-02 2.50e+03 9.45e-02 1.12e+02 pdb=" CG ASN B 611 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.142 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 448 " 0.072 2.00e-02 2.50e+03 7.52e-02 7.06e+01 pdb=" CG ASN G 448 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN G 448 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN G 448 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 301 " 0.070 2.00e-02 2.50e+03 7.10e-02 6.31e+01 pdb=" CG ASN G 301 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN G 301 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG G 606 " 0.085 2.00e-02 2.50e+03 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 43 2.38 - 3.01: 10585 3.01 - 3.64: 24239 3.64 - 4.27: 40449 4.27 - 4.90: 65636 Nonbonded interactions: 140952 Sorted by model distance: nonbonded pdb=" C6 NAG V 1 " pdb=" C6 NAG E 608 " model vdw 1.753 3.840 nonbonded pdb=" C8 NAG R 2 " pdb=" O3 NAG R 2 " model vdw 1.873 3.460 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 1.887 3.040 nonbonded pdb=" C8 NAG j 1 " pdb=" O3 NAG j 1 " model vdw 1.887 3.460 nonbonded pdb=" C8 NAG G 606 " pdb=" O3 NAG G 606 " model vdw 1.892 3.460 ... (remaining 140947 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = (chain 'B' and resid 520 through 703) selection = (chain 'D' and resid 520 through 703) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 32 through 57 or resid 66 through 504 or resid 602 through \ 610)) selection = (chain 'E' and (resid 32 through 57 or resid 66 through 397 or resid 412 through \ 504 or resid 601 through 609)) selection = (chain 'G' and (resid 32 through 184 or resid 189 through 397 or resid 412 throu \ gh 504 or resid 603 through 611)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.040 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.013 0.224 18838 Z= 0.706 Angle : 1.559 44.703 25751 Z= 0.903 Chirality : 0.083 1.317 3104 Planarity : 0.005 0.034 3122 Dihedral : 12.392 109.482 8386 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Rotamer: Outliers : 0.74 % Allowed : 0.74 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.18), residues: 2113 helix: 0.36 (0.22), residues: 373 sheet: 1.35 (0.19), residues: 605 loop : 2.51 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.030 0.004 TYR C 191 PHE 0.025 0.004 PHE I 98 TRP 0.029 0.005 TRP G 479 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.01201 (18703) covalent geometry : angle 1.48432 (25383) SS BOND : bond 0.07335 ( 37) SS BOND : angle 3.17748 ( 74) hydrogen bonds : bond 0.20495 ( 669) hydrogen bonds : angle 7.66030 ( 1866) link_ALPHA1-3 : bond 0.00766 ( 2) link_ALPHA1-3 : angle 6.84489 ( 6) link_BETA1-4 : bond 0.05589 ( 30) link_BETA1-4 : angle 6.20749 ( 90) link_NAG-ASN : bond 0.07211 ( 66) link_NAG-ASN : angle 3.30019 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 364 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5924 (m-40) cc_final: 0.5666 (p0) REVERT: C 180 ASP cc_start: 0.8615 (m-30) cc_final: 0.8251 (m-30) REVERT: E 161 MET cc_start: 0.8557 (tpt) cc_final: 0.8274 (tpt) REVERT: E 377 ASN cc_start: 0.8798 (t0) cc_final: 0.8499 (t0) REVERT: L 6 GLN cc_start: 0.6429 (tt0) cc_final: 0.6097 (tt0) REVERT: L 29 VAL cc_start: 0.8189 (m) cc_final: 0.7977 (p) REVERT: L 87 PHE cc_start: 0.8325 (m-80) cc_final: 0.8060 (m-80) REVERT: F 574 LYS cc_start: 0.9062 (mttt) cc_final: 0.8687 (mmtt) REVERT: G 125 LEU cc_start: 0.8615 (mt) cc_final: 0.8140 (tp) REVERT: G 504 ARG cc_start: 0.5583 (mtt180) cc_final: 0.4480 (mmt180) REVERT: A 79 TYR cc_start: 0.7226 (m-80) cc_final: 0.6935 (m-80) outliers start: 14 outliers final: 8 residues processed: 376 average time/residue: 0.1311 time to fit residues: 73.1055 Evaluate side-chains 172 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 195 ASN C 422 GLN C 425 ASN D 540 GLN D 543 ASN D 590 GLN E 195 ASN L 42 GLN L 89 GLN H 13 GLN H 100 HIS G 377 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.089891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075506 restraints weight = 55502.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077617 restraints weight = 33108.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079047 restraints weight = 23288.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079950 restraints weight = 18227.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080647 restraints weight = 15463.190| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18838 Z= 0.164 Angle : 1.058 43.748 25751 Z= 0.452 Chirality : 0.052 0.640 3104 Planarity : 0.005 0.066 3122 Dihedral : 9.042 83.979 4369 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Rotamer: Outliers : 1.90 % Allowed : 6.39 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.17), residues: 2113 helix: 1.61 (0.26), residues: 386 sheet: 0.79 (0.20), residues: 578 loop : 1.44 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.017 0.001 TYR A 32 PHE 0.039 0.002 PHE E 53 TRP 0.025 0.001 TRP G 479 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00350 (18703) covalent geometry : angle 1.02326 (25383) SS BOND : bond 0.00342 ( 37) SS BOND : angle 1.33583 ( 74) hydrogen bonds : bond 0.05434 ( 669) hydrogen bonds : angle 5.63327 ( 1866) link_ALPHA1-3 : bond 0.02499 ( 2) link_ALPHA1-3 : angle 4.44712 ( 6) link_BETA1-4 : bond 0.00665 ( 30) link_BETA1-4 : angle 2.10669 ( 90) link_NAG-ASN : bond 0.00590 ( 66) link_NAG-ASN : angle 2.83479 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 647 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7983 (mt-10) REVERT: B 655 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7354 (ttpt) REVERT: B 656 ASN cc_start: 0.5715 (m-40) cc_final: 0.5376 (p0) REVERT: C 50 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 180 ASP cc_start: 0.8347 (m-30) cc_final: 0.7969 (m-30) REVERT: E 377 ASN cc_start: 0.8439 (t0) cc_final: 0.8023 (t0) REVERT: E 424 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8982 (mt) REVERT: L 6 GLN cc_start: 0.6620 (tt0) cc_final: 0.6384 (tt0) REVERT: L 87 PHE cc_start: 0.8500 (m-80) cc_final: 0.8299 (m-80) REVERT: F 574 LYS cc_start: 0.8906 (mttt) cc_final: 0.8547 (mmtt) REVERT: G 504 ARG cc_start: 0.5752 (mtt180) cc_final: 0.4368 (mmt180) REVERT: A 29 LEU cc_start: 0.8255 (tp) cc_final: 0.7920 (tt) outliers start: 36 outliers final: 26 residues processed: 224 average time/residue: 0.1142 time to fit residues: 40.3314 Evaluate side-chains 195 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 82 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 53 ASN L 89 GLN H 100 HIS F 625 ASN G 105 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069364 restraints weight = 57616.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071315 restraints weight = 34856.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072614 restraints weight = 24835.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073532 restraints weight = 19753.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074095 restraints weight = 16790.322| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18838 Z= 0.229 Angle : 1.038 43.689 25751 Z= 0.444 Chirality : 0.052 0.666 3104 Planarity : 0.005 0.072 3122 Dihedral : 8.164 79.634 4361 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 2.69 % Allowed : 6.66 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2113 helix: 1.45 (0.26), residues: 392 sheet: 0.57 (0.20), residues: 602 loop : 0.69 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.017 0.002 TYR A 91 PHE 0.031 0.003 PHE E 53 TRP 0.016 0.002 TRP B 610 HIS 0.043 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00531 (18703) covalent geometry : angle 1.00073 (25383) SS BOND : bond 0.00643 ( 37) SS BOND : angle 1.75692 ( 74) hydrogen bonds : bond 0.05137 ( 669) hydrogen bonds : angle 5.38124 ( 1866) link_ALPHA1-3 : bond 0.02252 ( 2) link_ALPHA1-3 : angle 3.80632 ( 6) link_BETA1-4 : bond 0.00572 ( 30) link_BETA1-4 : angle 2.10188 ( 90) link_NAG-ASN : bond 0.00581 ( 66) link_NAG-ASN : angle 2.83446 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5651 (m-40) cc_final: 0.5232 (p0) REVERT: C 180 ASP cc_start: 0.8392 (m-30) cc_final: 0.8112 (m-30) REVERT: D 540 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: E 424 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9203 (mt) REVERT: L 6 GLN cc_start: 0.6652 (tt0) cc_final: 0.6434 (tt0) REVERT: L 29 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8162 (t) REVERT: L 87 PHE cc_start: 0.8423 (m-80) cc_final: 0.8205 (m-80) REVERT: F 574 LYS cc_start: 0.8913 (mttt) cc_final: 0.8539 (mmtt) REVERT: G 301 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7784 (t0) REVERT: G 504 ARG cc_start: 0.5816 (mtt180) cc_final: 0.4475 (mmt180) outliers start: 51 outliers final: 36 residues processed: 201 average time/residue: 0.1112 time to fit residues: 35.3813 Evaluate side-chains 181 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 374 HIS C 425 ASN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN H 39 GLN F 625 ASN G 330 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.084122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069565 restraints weight = 57175.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071520 restraints weight = 34718.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072857 restraints weight = 24791.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073770 restraints weight = 19649.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074393 restraints weight = 16732.675| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18838 Z= 0.155 Angle : 0.968 43.543 25751 Z= 0.402 Chirality : 0.049 0.548 3104 Planarity : 0.004 0.057 3122 Dihedral : 7.735 79.024 4361 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 2.11 % Allowed : 7.87 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2113 helix: 1.54 (0.27), residues: 398 sheet: 0.46 (0.20), residues: 575 loop : 0.43 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 18 TYR 0.013 0.001 TYR F 586 PHE 0.029 0.002 PHE E 53 TRP 0.014 0.001 TRP B 610 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00350 (18703) covalent geometry : angle 0.93561 (25383) SS BOND : bond 0.00345 ( 37) SS BOND : angle 1.34352 ( 74) hydrogen bonds : bond 0.04336 ( 669) hydrogen bonds : angle 5.16944 ( 1866) link_ALPHA1-3 : bond 0.02402 ( 2) link_ALPHA1-3 : angle 3.72262 ( 6) link_BETA1-4 : bond 0.00536 ( 30) link_BETA1-4 : angle 1.95202 ( 90) link_NAG-ASN : bond 0.00418 ( 66) link_NAG-ASN : angle 2.60488 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5615 (m-40) cc_final: 0.5217 (p0) REVERT: C 180 ASP cc_start: 0.8377 (m-30) cc_final: 0.8148 (m-30) REVERT: D 535 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6655 (tmm) REVERT: D 540 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: E 377 ASN cc_start: 0.8434 (t0) cc_final: 0.8140 (t0) REVERT: E 424 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9204 (mt) REVERT: L 6 GLN cc_start: 0.6780 (tt0) cc_final: 0.6523 (tt0) REVERT: L 29 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7881 (t) REVERT: L 80 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7387 (tm-30) REVERT: L 87 PHE cc_start: 0.8249 (m-80) cc_final: 0.8021 (m-80) REVERT: F 574 LYS cc_start: 0.8871 (mttt) cc_final: 0.8506 (mmtt) REVERT: G 301 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7883 (t0) REVERT: G 376 PHE cc_start: 0.8119 (m-80) cc_final: 0.7840 (m-10) REVERT: G 504 ARG cc_start: 0.5766 (mtt180) cc_final: 0.4512 (mmt180) REVERT: A 18 MET cc_start: 0.5699 (ttm) cc_final: 0.5266 (ttt) outliers start: 40 outliers final: 29 residues processed: 187 average time/residue: 0.1144 time to fit residues: 33.8308 Evaluate side-chains 174 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 64 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 58 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 422 GLN E 195 ASN L 76 HIS F 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.066640 restraints weight = 57599.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068486 restraints weight = 35353.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069742 restraints weight = 25468.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070616 restraints weight = 20420.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071201 restraints weight = 17475.001| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18838 Z= 0.228 Angle : 1.010 43.533 25751 Z= 0.429 Chirality : 0.050 0.464 3104 Planarity : 0.005 0.061 3122 Dihedral : 8.102 80.912 4359 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 2.85 % Allowed : 8.72 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2113 helix: 1.37 (0.26), residues: 398 sheet: 0.35 (0.20), residues: 589 loop : -0.04 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 71 TYR 0.020 0.002 TYR H 98 PHE 0.026 0.003 PHE E 53 TRP 0.014 0.002 TRP B 610 HIS 0.033 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00532 (18703) covalent geometry : angle 0.97818 (25383) SS BOND : bond 0.00374 ( 37) SS BOND : angle 1.60052 ( 74) hydrogen bonds : bond 0.04722 ( 669) hydrogen bonds : angle 5.27705 ( 1866) link_ALPHA1-3 : bond 0.02231 ( 2) link_ALPHA1-3 : angle 3.52605 ( 6) link_BETA1-4 : bond 0.00510 ( 30) link_BETA1-4 : angle 1.95189 ( 90) link_NAG-ASN : bond 0.00502 ( 66) link_NAG-ASN : angle 2.65766 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 535 MET cc_start: 0.7054 (mpp) cc_final: 0.6485 (tmm) REVERT: D 540 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: E 377 ASN cc_start: 0.8610 (t0) cc_final: 0.8332 (t0) REVERT: L 6 GLN cc_start: 0.6910 (tt0) cc_final: 0.6567 (tt0) REVERT: H 32 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.5056 (t80) REVERT: F 530 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: F 574 LYS cc_start: 0.8840 (mttt) cc_final: 0.8435 (mmtt) REVERT: F 633 LYS cc_start: 0.8991 (pttp) cc_final: 0.8395 (mttp) REVERT: G 301 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7998 (t0) REVERT: G 504 ARG cc_start: 0.5918 (mtt180) cc_final: 0.4586 (mmt180) REVERT: I 3 VAL cc_start: 0.8536 (t) cc_final: 0.8298 (m) REVERT: A 82 ASN cc_start: 0.8604 (t0) cc_final: 0.8359 (t0) outliers start: 54 outliers final: 40 residues processed: 189 average time/residue: 0.1198 time to fit residues: 35.2639 Evaluate side-chains 175 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 116 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 184 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS E 377 ASN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.083009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068717 restraints weight = 56499.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070612 restraints weight = 34404.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071913 restraints weight = 24628.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.072798 restraints weight = 19533.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073392 restraints weight = 16645.215| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18838 Z= 0.122 Angle : 0.937 43.471 25751 Z= 0.383 Chirality : 0.048 0.432 3104 Planarity : 0.004 0.053 3122 Dihedral : 7.520 80.924 4359 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 1.80 % Allowed : 10.14 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2113 helix: 1.63 (0.27), residues: 399 sheet: 0.39 (0.20), residues: 571 loop : 0.05 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 75 TYR 0.014 0.001 TYR A 32 PHE 0.026 0.001 PHE E 53 TRP 0.014 0.001 TRP A 103 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00265 (18703) covalent geometry : angle 0.90926 (25383) SS BOND : bond 0.00283 ( 37) SS BOND : angle 1.29656 ( 74) hydrogen bonds : bond 0.03827 ( 669) hydrogen bonds : angle 4.94664 ( 1866) link_ALPHA1-3 : bond 0.02397 ( 2) link_ALPHA1-3 : angle 3.69291 ( 6) link_BETA1-4 : bond 0.00562 ( 30) link_BETA1-4 : angle 1.77611 ( 90) link_NAG-ASN : bond 0.00422 ( 66) link_NAG-ASN : angle 2.39923 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5421 (m-40) cc_final: 0.5075 (p0) REVERT: D 535 MET cc_start: 0.6871 (mpp) cc_final: 0.6249 (tmm) REVERT: D 540 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: L 6 GLN cc_start: 0.6949 (tt0) cc_final: 0.6534 (tt0) REVERT: L 78 MET cc_start: 0.7787 (tpt) cc_final: 0.7459 (ttt) REVERT: H 32 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4678 (t80) REVERT: H 35 ASN cc_start: 0.8918 (m-40) cc_final: 0.8642 (m-40) REVERT: F 574 LYS cc_start: 0.8776 (mttt) cc_final: 0.8347 (mmtt) REVERT: F 633 LYS cc_start: 0.8990 (pttp) cc_final: 0.8345 (mttt) REVERT: G 301 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7941 (t0) REVERT: G 376 PHE cc_start: 0.8053 (m-80) cc_final: 0.7838 (m-10) REVERT: G 504 ARG cc_start: 0.5945 (mtt180) cc_final: 0.4620 (mmt180) REVERT: I 3 VAL cc_start: 0.8439 (t) cc_final: 0.8080 (m) REVERT: A 82 ASN cc_start: 0.8657 (t0) cc_final: 0.8314 (t0) outliers start: 34 outliers final: 27 residues processed: 172 average time/residue: 0.1176 time to fit residues: 32.5615 Evaluate side-chains 169 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.3980 chunk 33 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS E 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.067443 restraints weight = 57557.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069243 restraints weight = 35583.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070512 restraints weight = 25760.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071369 restraints weight = 20599.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071955 restraints weight = 17621.738| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18838 Z= 0.158 Angle : 0.951 43.476 25751 Z= 0.392 Chirality : 0.048 0.394 3104 Planarity : 0.004 0.057 3122 Dihedral : 7.536 83.331 4359 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.93 % Rotamer: Outliers : 2.17 % Allowed : 10.35 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2113 helix: 1.60 (0.27), residues: 401 sheet: 0.42 (0.21), residues: 569 loop : -0.10 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.019 0.001 TYR A 32 PHE 0.024 0.002 PHE E 53 TRP 0.012 0.001 TRP A 33 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00365 (18703) covalent geometry : angle 0.92283 (25383) SS BOND : bond 0.00283 ( 37) SS BOND : angle 1.44371 ( 74) hydrogen bonds : bond 0.04033 ( 669) hydrogen bonds : angle 4.90260 ( 1866) link_ALPHA1-3 : bond 0.02185 ( 2) link_ALPHA1-3 : angle 3.55052 ( 6) link_BETA1-4 : bond 0.00469 ( 30) link_BETA1-4 : angle 1.74760 ( 90) link_NAG-ASN : bond 0.00402 ( 66) link_NAG-ASN : angle 2.40734 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5405 (m-40) cc_final: 0.5065 (p0) REVERT: C 125 LEU cc_start: 0.9160 (tp) cc_final: 0.8956 (tp) REVERT: D 535 MET cc_start: 0.6974 (mpp) cc_final: 0.6724 (tmm) REVERT: D 540 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: E 307 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8594 (pt) REVERT: L 6 GLN cc_start: 0.6955 (tt0) cc_final: 0.6588 (tt0) REVERT: H 32 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.4855 (t80) REVERT: H 75 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8364 (mtt180) REVERT: F 574 LYS cc_start: 0.8780 (mttt) cc_final: 0.8357 (mmtt) REVERT: F 633 LYS cc_start: 0.8990 (pttp) cc_final: 0.8342 (mttt) REVERT: G 504 ARG cc_start: 0.6031 (mtt180) cc_final: 0.4690 (mmt180) REVERT: A 43 LYS cc_start: 0.7526 (mttt) cc_final: 0.7161 (pttm) REVERT: A 82 ASN cc_start: 0.8697 (t0) cc_final: 0.8387 (t0) outliers start: 41 outliers final: 31 residues processed: 174 average time/residue: 0.1223 time to fit residues: 33.9723 Evaluate side-chains 170 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 94 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 185 optimal weight: 0.0980 chunk 130 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066377 restraints weight = 57597.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068175 restraints weight = 35970.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069405 restraints weight = 26143.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070204 restraints weight = 21059.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070786 restraints weight = 18234.495| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18838 Z= 0.190 Angle : 0.976 43.516 25751 Z= 0.405 Chirality : 0.049 0.376 3104 Planarity : 0.004 0.049 3122 Dihedral : 7.670 86.267 4359 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 2.48 % Allowed : 10.09 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2113 helix: 1.51 (0.27), residues: 401 sheet: 0.38 (0.21), residues: 565 loop : -0.24 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.023 0.002 TYR A 32 PHE 0.022 0.002 PHE E 53 TRP 0.013 0.001 TRP A 33 HIS 0.013 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00441 (18703) covalent geometry : angle 0.94577 (25383) SS BOND : bond 0.00373 ( 37) SS BOND : angle 1.43358 ( 74) hydrogen bonds : bond 0.04171 ( 669) hydrogen bonds : angle 4.97732 ( 1866) link_ALPHA1-3 : bond 0.02215 ( 2) link_ALPHA1-3 : angle 3.49479 ( 6) link_BETA1-4 : bond 0.00475 ( 30) link_BETA1-4 : angle 1.76433 ( 90) link_NAG-ASN : bond 0.00435 ( 66) link_NAG-ASN : angle 2.56703 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.7824 (mmm) cc_final: 0.7558 (mmt) REVERT: D 540 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: E 307 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8601 (pt) REVERT: E 430 ILE cc_start: 0.8535 (mm) cc_final: 0.8222 (mp) REVERT: L 6 GLN cc_start: 0.7008 (tt0) cc_final: 0.6602 (tt0) REVERT: L 78 MET cc_start: 0.7748 (tpt) cc_final: 0.7446 (ttt) REVERT: H 32 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5003 (t80) REVERT: H 75 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8414 (mtt180) REVERT: F 574 LYS cc_start: 0.8791 (mttt) cc_final: 0.8312 (mmtt) REVERT: F 633 LYS cc_start: 0.9030 (pttp) cc_final: 0.8383 (mttt) REVERT: G 504 ARG cc_start: 0.6141 (mtt180) cc_final: 0.4745 (mmt180) REVERT: A 43 LYS cc_start: 0.7589 (mttt) cc_final: 0.7179 (pttm) REVERT: A 82 ASN cc_start: 0.8697 (t0) cc_final: 0.8333 (t0) outliers start: 47 outliers final: 40 residues processed: 177 average time/residue: 0.1240 time to fit residues: 34.7891 Evaluate side-chains 179 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 14 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067673 restraints weight = 57355.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069511 restraints weight = 35535.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070777 restraints weight = 25649.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071640 restraints weight = 20538.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072229 restraints weight = 17565.787| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18838 Z= 0.127 Angle : 0.942 43.446 25751 Z= 0.386 Chirality : 0.047 0.360 3104 Planarity : 0.004 0.053 3122 Dihedral : 7.396 87.119 4359 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.01 % Allowed : 10.94 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 2113 helix: 1.86 (0.28), residues: 384 sheet: 0.39 (0.21), residues: 566 loop : -0.23 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.018 0.001 TYR A 32 PHE 0.023 0.001 PHE E 53 TRP 0.012 0.001 TRP A 47 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00285 (18703) covalent geometry : angle 0.91585 (25383) SS BOND : bond 0.00311 ( 37) SS BOND : angle 1.32448 ( 74) hydrogen bonds : bond 0.03720 ( 669) hydrogen bonds : angle 4.81207 ( 1866) link_ALPHA1-3 : bond 0.02204 ( 2) link_ALPHA1-3 : angle 3.59132 ( 6) link_BETA1-4 : bond 0.00521 ( 30) link_BETA1-4 : angle 1.69469 ( 90) link_NAG-ASN : bond 0.00432 ( 66) link_NAG-ASN : angle 2.36936 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.7785 (mmm) cc_final: 0.7472 (mmt) REVERT: B 656 ASN cc_start: 0.5296 (m-40) cc_final: 0.4958 (p0) REVERT: D 540 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6044 (mp-120) REVERT: E 430 ILE cc_start: 0.8484 (mm) cc_final: 0.8194 (mp) REVERT: L 6 GLN cc_start: 0.6975 (tt0) cc_final: 0.6519 (tt0) REVERT: H 32 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.4849 (t80) REVERT: H 75 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8395 (mtt180) REVERT: F 574 LYS cc_start: 0.8751 (mttt) cc_final: 0.8278 (mmtt) REVERT: F 633 LYS cc_start: 0.8997 (pttp) cc_final: 0.8388 (mttt) REVERT: G 504 ARG cc_start: 0.6163 (mtt180) cc_final: 0.4781 (mmt180) REVERT: A 43 LYS cc_start: 0.7571 (mttt) cc_final: 0.7221 (pttm) REVERT: A 82 ASN cc_start: 0.8725 (t0) cc_final: 0.8394 (t0) outliers start: 38 outliers final: 31 residues processed: 171 average time/residue: 0.1229 time to fit residues: 33.6723 Evaluate side-chains 171 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 162 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** 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 = 0.3613 r_free = 0.3613 target = 0.082478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068199 restraints weight = 57115.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.070011 restraints weight = 35256.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071308 restraints weight = 25458.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072175 restraints weight = 20284.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072765 restraints weight = 17325.895| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18838 Z= 0.119 Angle : 0.932 43.419 25751 Z= 0.380 Chirality : 0.047 0.353 3104 Planarity : 0.004 0.047 3122 Dihedral : 7.224 88.089 4359 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 1.74 % Allowed : 11.15 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2113 helix: 1.93 (0.28), residues: 384 sheet: 0.43 (0.21), residues: 556 loop : -0.21 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.018 0.001 TYR A 32 PHE 0.023 0.001 PHE E 53 TRP 0.013 0.001 TRP A 47 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00264 (18703) covalent geometry : angle 0.90826 (25383) SS BOND : bond 0.00274 ( 37) SS BOND : angle 1.29949 ( 74) hydrogen bonds : bond 0.03517 ( 669) hydrogen bonds : angle 4.70275 ( 1866) link_ALPHA1-3 : bond 0.02302 ( 2) link_ALPHA1-3 : angle 3.52906 ( 6) link_BETA1-4 : bond 0.00509 ( 30) link_BETA1-4 : angle 1.64398 ( 90) link_NAG-ASN : bond 0.00450 ( 66) link_NAG-ASN : angle 2.25043 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5400 (m-40) cc_final: 0.4933 (p0) REVERT: C 142 MET cc_start: 0.2657 (mmm) cc_final: 0.0468 (ttt) REVERT: D 540 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.6062 (mp-120) REVERT: D 633 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (pptt) REVERT: E 430 ILE cc_start: 0.8507 (mm) cc_final: 0.8211 (mp) REVERT: L 6 GLN cc_start: 0.7007 (tt0) cc_final: 0.6504 (tt0) REVERT: H 32 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4593 (t80) REVERT: H 75 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8404 (mtt180) REVERT: F 574 LYS cc_start: 0.8731 (mttt) cc_final: 0.8264 (mmtt) REVERT: F 633 LYS cc_start: 0.9017 (pttp) cc_final: 0.8390 (mttt) REVERT: G 504 ARG cc_start: 0.6103 (mtt180) cc_final: 0.4742 (mmt180) REVERT: A 43 LYS cc_start: 0.7682 (mttt) cc_final: 0.7264 (pttm) REVERT: A 77 THR cc_start: 0.7456 (p) cc_final: 0.7024 (p) REVERT: A 82 ASN cc_start: 0.8726 (t0) cc_final: 0.8410 (t0) outliers start: 33 outliers final: 28 residues processed: 171 average time/residue: 0.1246 time to fit residues: 34.0388 Evaluate side-chains 169 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 149 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 chunk 151 optimal weight: 0.2980 chunk 122 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 0.0000 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** 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 = 0.3640 r_free = 0.3640 target = 0.083888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069670 restraints weight = 56417.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071588 restraints weight = 34103.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072888 restraints weight = 24200.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073799 restraints weight = 19142.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074415 restraints weight = 16235.148| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18838 Z= 0.103 Angle : 0.917 43.453 25751 Z= 0.373 Chirality : 0.046 0.346 3104 Planarity : 0.004 0.051 3122 Dihedral : 7.025 88.371 4359 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.74 % Allowed : 11.36 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2113 helix: 2.17 (0.28), residues: 379 sheet: 0.48 (0.21), residues: 563 loop : -0.20 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 308 TYR 0.011 0.001 TYR F 586 PHE 0.023 0.001 PHE E 53 TRP 0.016 0.001 TRP A 47 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00220 (18703) covalent geometry : angle 0.89600 (25383) SS BOND : bond 0.00243 ( 37) SS BOND : angle 1.18472 ( 74) hydrogen bonds : bond 0.03223 ( 669) hydrogen bonds : angle 4.57056 ( 1866) link_ALPHA1-3 : bond 0.02309 ( 2) link_ALPHA1-3 : angle 3.52676 ( 6) link_BETA1-4 : bond 0.00537 ( 30) link_BETA1-4 : angle 1.59590 ( 90) link_NAG-ASN : bond 0.00415 ( 66) link_NAG-ASN : angle 2.11858 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.67 seconds wall clock time: 47 minutes 20.51 seconds (2840.51 seconds total)