Starting phenix.real_space_refine on Sat Jul 4 04:55:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_25376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq1_25376/07_2026/7sq1_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-dev-6108/lib/python3.11/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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 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 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 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 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 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 chiralities: 11 Time building chain proxies: 3.68, per 1000 atoms: 0.20 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: 2.10 Conformation dependent library (CDL) restraints added in 887.3 milliseconds 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: 0.87 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: 3.21 Time building geometry restraints manager: 2.61 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 - 17.46: 9991 17.46 - 34.91: 303 34.91 - 52.37: 95 52.37 - 69.83: 46 69.83 - 87.29: 20 Dihedral angle restraints: 10455 sinusoidal: 4245 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 10452 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: 13.860 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.180 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 11.325 87.287 6342 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 are 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/Z covalent geometry : bond 0.01201 / 0.65 (18703) covalent geometry : angle 1.48432 / 0.89 (25383) SS BOND : bond 0.07335 / 4.50 ( 37) SS BOND : angle 3.17748 / 2.17 ( 74) hydrogen bonds : bond 0.20495 / 13.54 ( 669) hydrogen bonds : angle 7.66030 / 5.45 ( 1866) link_ALPHA1-3 : bond 0.00766 / 0.39 ( 2) link_ALPHA1-3 : angle 6.84489 / 2.62 ( 6) link_BETA1-4 : bond 0.05589 / 3.33 ( 30) link_BETA1-4 : angle 6.20749 / 4.00 ( 90) link_NAG-ASN : bond 0.07211 / 4.77 ( 66) link_NAG-ASN : angle 3.30019 / 2.45 ( 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 : 0.651 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: 0.8556 (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: 0.9063 (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: 0.7225 (m-80) cc_final: 0.6935 (m-80) outliers start: 14 outliers final: 8 residues processed: 376 average time/residue: 0.1405 time to fit residues: 78.3202 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 : 0.702 ------------------------------------------------------------------------------- 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... 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 89 GLN H 13 GLN H 100 HIS G 377 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.089949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075519 restraints weight = 55472.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077625 restraints weight = 33145.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079060 restraints weight = 23360.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080039 restraints weight = 18297.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080679 restraints weight = 15410.074| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18838 Z= 0.166 Angle : 1.059 43.600 25751 Z= 0.453 Chirality : 0.053 0.814 3104 Planarity : 0.005 0.069 3122 Dihedral : 5.980 83.586 2325 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Rotamer: Outliers : 1.95 % Allowed : 6.29 % Favored : 91.76 % 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 are not related in a simple way. whole: 1.80 (0.17), residues: 2113 helix: 1.67 (0.26), residues: 386 sheet: 0.81 (0.19), residues: 578 loop : 1.47 (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 0.041 0.002 PHE E 53 TRP 0.024 0.001 TRP G 479 HIS 0.005 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (18703) covalent geometry : angle 1.02470 / 0.44 (25383) SS BOND : bond 0.00400 / 0.27 ( 37) SS BOND : angle 1.39734 / 0.96 ( 74) hydrogen bonds : bond 0.05720 / 3.82 ( 669) hydrogen bonds : angle 5.67971 / 4.01 ( 1866) link_ALPHA1-3 : bond 0.03244 / 1.71 ( 2) link_ALPHA1-3 : angle 3.13298 / 1.43 ( 6) link_BETA1-4 : bond 0.00660 / 0.41 ( 30) link_BETA1-4 : angle 2.00403 / 1.31 ( 90) link_NAG-ASN : bond 0.00521 / 0.37 ( 66) link_NAG-ASN : angle 2.91140 / 2.22 ( 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 240 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.662 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: 0.5752 (m-40) cc_final: 0.5486 (p0) REVERT: C 50 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 180 ASP cc_start: 0.8353 (m-30) cc_final: 0.7976 (m-30) REVERT: E 377 ASN cc_start: 0.8445 (t0) cc_final: 0.8037 (t0) REVERT: E 424 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.8962 (mt) REVERT: L 6 GLN cc_start: 0.6621 (tt0) cc_final: 0.6384 (tt0) REVERT: L 82 ASP cc_start: 0.7839 (m-30) cc_final: 0.7516 (m-30) REVERT: F 574 LYS cc_start: 0.8890 (mttt) cc_final: 0.8564 (mmtt) REVERT: G 504 ARG cc_start: 0.5777 (mtt180) cc_final: 0.4380 (mmt180) REVERT: A 29 LEU cc_start: 0.8214 (tp) cc_final: 0.7887 (tt) outliers start: 37 outliers final: 27 residues processed: 224 average time/residue: 0.1329 time to fit residues: 46.7903 Evaluate side-chains 191 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 H residue 98 TYR 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: 3.9990 chunk 92 optimal weight: 5.9990 chunk 187 optimal weight: 0.0770 chunk 172 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 374 HIS E 136 ASN ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3652 r_free = 0.3652 target = 0.084480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069926 restraints weight = 57529.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071893 restraints weight = 34781.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073231 restraints weight = 24817.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074139 restraints weight = 19685.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.074700 restraints weight = 16765.553| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18838 Z= 0.205 Angle : 1.023 43.629 25751 Z= 0.436 Chirality : 0.050 0.649 3104 Planarity : 0.005 0.073 3122 Dihedral : 5.845 79.345 2319 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 2.75 % Allowed : 6.92 % Favored : 90.33 % 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 are not related in a simple way. whole: 1.08 (0.17), residues: 2113 helix: 1.53 (0.27), residues: 392 sheet: 0.48 (0.20), residues: 573 loop : 0.71 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.017 0.002 TYR F 586 PHE 0.030 0.003 PHE E 53 TRP 0.017 0.002 TRP D 623 HIS 0.045 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (18703) covalent geometry : angle 0.98880 / 0.43 (25383) SS BOND : bond 0.00497 / 0.34 ( 37) SS BOND : angle 1.76207 / 1.23 ( 74) hydrogen bonds : bond 0.04917 / 3.25 ( 669) hydrogen bonds : angle 5.34645 / 3.77 ( 1866) link_ALPHA1-3 : bond 0.01481 / 0.78 ( 2) link_ALPHA1-3 : angle 3.09717 / 1.28 ( 6) link_BETA1-4 : bond 0.00558 / 0.36 ( 30) link_BETA1-4 : angle 1.91786 / 1.28 ( 90) link_NAG-ASN : bond 0.00525 / 0.34 ( 66) link_NAG-ASN : angle 2.78256 / 2.07 ( 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 219 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.723 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: B 656 ASN cc_start: 0.5850 (m-40) cc_final: 0.5390 (p0) REVERT: C 180 ASP cc_start: 0.8384 (m-30) cc_final: 0.8088 (m-30) REVERT: D 540 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: E 424 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9185 (mt) REVERT: L 29 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8123 (t) REVERT: F 574 LYS cc_start: 0.8883 (mttt) cc_final: 0.8529 (mmtt) REVERT: F 633 LYS cc_start: 0.8962 (pttp) cc_final: 0.8395 (mttp) REVERT: G 301 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7860 (t0) REVERT: G 376 PHE cc_start: 0.8236 (m-80) cc_final: 0.7974 (m-10) REVERT: G 504 ARG cc_start: 0.5814 (mtt180) cc_final: 0.4473 (mmt180) outliers start: 52 outliers final: 38 residues processed: 201 average time/residue: 0.1320 time to fit residues: 41.7830 Evaluate side-chains 185 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 392 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN 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 612 SER Chi-restraints excluded: chain D residue 647 GLU 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 32 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 I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 166 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 193 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 425 ASN L 38 GLN H 39 GLN F 625 ASN G 330 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.068699 restraints weight = 57511.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070595 restraints weight = 35008.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071876 restraints weight = 25081.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072773 restraints weight = 19995.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073329 restraints weight = 17050.243| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18838 Z= 0.186 Angle : 0.980 43.861 25751 Z= 0.412 Chirality : 0.048 0.496 3104 Planarity : 0.004 0.058 3122 Dihedral : 5.731 78.341 2317 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 2.54 % Allowed : 7.61 % Favored : 89.86 % 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 are not related in a simple way. whole: 0.79 (0.17), residues: 2113 helix: 1.49 (0.27), residues: 398 sheet: 0.45 (0.20), residues: 592 loop : 0.34 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 18 TYR 0.014 0.002 TYR A 91 PHE 0.028 0.002 PHE E 53 TRP 0.014 0.001 TRP B 610 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (18703) covalent geometry : angle 0.95045 / 0.40 (25383) SS BOND : bond 0.00578 / 0.42 ( 37) SS BOND : angle 1.35155 / 0.97 ( 74) hydrogen bonds : bond 0.04505 / 2.99 ( 669) hydrogen bonds : angle 5.20967 / 3.67 ( 1866) link_ALPHA1-3 : bond 0.00750 / 0.39 ( 2) link_ALPHA1-3 : angle 2.53781 / 1.08 ( 6) link_BETA1-4 : bond 0.00527 / 0.34 ( 30) link_BETA1-4 : angle 1.83721 / 1.22 ( 90) link_NAG-ASN : bond 0.00405 / 0.27 ( 66) link_NAG-ASN : angle 2.60984 / 1.94 ( 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 199 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.649 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: B 656 ASN cc_start: 0.5735 (m-40) cc_final: 0.5303 (p0) REVERT: C 180 ASP cc_start: 0.8401 (m-30) cc_final: 0.8172 (m-30) REVERT: D 540 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: E 377 ASN cc_start: 0.8453 (t0) cc_final: 0.8177 (t0) REVERT: E 424 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9199 (mt) REVERT: L 29 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7928 (t) REVERT: L 80 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7394 (tm-30) REVERT: F 574 LYS cc_start: 0.8881 (mttt) cc_final: 0.8490 (mmtt) REVERT: F 633 LYS cc_start: 0.9065 (pttp) cc_final: 0.8384 (mttt) REVERT: G 301 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7849 (t0) REVERT: G 376 PHE cc_start: 0.8220 (m-80) cc_final: 0.7930 (m-10) REVERT: G 504 ARG cc_start: 0.5769 (mtt180) cc_final: 0.4505 (mmt180) outliers start: 48 outliers final: 36 residues processed: 186 average time/residue: 0.1273 time to fit residues: 37.7206 Evaluate side-chains 179 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 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 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 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 I residue 88 CYS 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: 1.9990 chunk 81 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS E 195 ASN L 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.066943 restraints weight = 57811.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068756 restraints weight = 36038.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069990 restraints weight = 26160.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070830 restraints weight = 21085.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071407 restraints weight = 18112.634| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18838 Z= 0.209 Angle : 0.989 43.564 25751 Z= 0.417 Chirality : 0.049 0.428 3104 Planarity : 0.004 0.060 3122 Dihedral : 5.744 80.798 2315 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.69 % Allowed : 8.77 % Favored : 88.54 % 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 are not related in a simple way. whole: 0.46 (0.17), residues: 2113 helix: 1.44 (0.26), residues: 398 sheet: 0.28 (0.20), residues: 591 loop : 0.01 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.017 0.002 TYR H 98 PHE 0.026 0.002 PHE E 53 TRP 0.014 0.001 TRP B 610 HIS 0.016 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (18703) covalent geometry : angle 0.96072 / 0.41 (25383) SS BOND : bond 0.00381 / 0.24 ( 37) SS BOND : angle 1.28753 / 0.91 ( 74) hydrogen bonds : bond 0.04585 / 3.05 ( 669) hydrogen bonds : angle 5.18959 / 3.65 ( 1866) link_ALPHA1-3 : bond 0.00612 / 0.32 ( 2) link_ALPHA1-3 : angle 2.08469 / 0.97 ( 6) link_BETA1-4 : bond 0.00519 / 0.34 ( 30) link_BETA1-4 : angle 1.79260 / 1.19 ( 90) link_NAG-ASN : bond 0.00428 / 0.28 ( 66) link_NAG-ASN : angle 2.59128 / 1.91 ( 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 197 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 125 LEU cc_start: 0.9266 (tp) cc_final: 0.8895 (tp) REVERT: D 540 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7672 (mp10) REVERT: E 377 ASN cc_start: 0.8608 (t0) cc_final: 0.8347 (t0) REVERT: L 80 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7416 (tm-30) REVERT: H 32 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.4908 (t80) REVERT: F 633 LYS cc_start: 0.9081 (pttp) cc_final: 0.8397 (mttt) REVERT: G 301 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7936 (t0) REVERT: G 376 PHE cc_start: 0.8257 (m-80) cc_final: 0.7937 (m-10) REVERT: G 504 ARG cc_start: 0.5921 (mtt180) cc_final: 0.4584 (mmt180) REVERT: A 82 ASN cc_start: 0.8579 (t0) cc_final: 0.8352 (t0) outliers start: 51 outliers final: 42 residues processed: 183 average time/residue: 0.1321 time to fit residues: 37.8057 Evaluate side-chains 179 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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 129 LEU 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 I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS 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: 3.9990 chunk 27 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS F 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068353 restraints weight = 56767.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070221 restraints weight = 35209.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071497 restraints weight = 25407.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072341 restraints weight = 20335.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072949 restraints weight = 17466.647| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18838 Z= 0.130 Angle : 0.936 43.477 25751 Z= 0.384 Chirality : 0.047 0.399 3104 Planarity : 0.004 0.052 3122 Dihedral : 5.475 81.746 2315 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 2.27 % Allowed : 9.35 % Favored : 88.38 % 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 are not related in a simple way. whole: 0.54 (0.18), residues: 2113 helix: 1.61 (0.27), residues: 399 sheet: 0.32 (0.20), residues: 569 loop : 0.02 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 617 TYR 0.014 0.001 TYR A 32 PHE 0.026 0.002 PHE E 53 TRP 0.013 0.001 TRP D 623 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18703) covalent geometry : angle 0.91129 / 0.38 (25383) SS BOND : bond 0.00295 / 0.20 ( 37) SS BOND : angle 1.07443 / 0.76 ( 74) hydrogen bonds : bond 0.03920 / 2.61 ( 669) hydrogen bonds : angle 4.93257 / 3.46 ( 1866) link_ALPHA1-3 : bond 0.00648 / 0.33 ( 2) link_ALPHA1-3 : angle 2.05146 / 0.95 ( 6) link_BETA1-4 : bond 0.00540 / 0.35 ( 30) link_BETA1-4 : angle 1.64642 / 1.10 ( 90) link_NAG-ASN : bond 0.00384 / 0.25 ( 66) link_NAG-ASN : angle 2.37516 / 1.78 ( 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 191 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.709 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: B 535 MET cc_start: 0.7731 (mmm) cc_final: 0.7484 (mmt) REVERT: B 656 ASN cc_start: 0.5473 (m-40) cc_final: 0.5109 (p0) REVERT: C 125 LEU cc_start: 0.9255 (tp) cc_final: 0.8833 (tp) REVERT: D 540 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: E 377 ASN cc_start: 0.8570 (t0) cc_final: 0.8318 (t0) REVERT: H 32 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.4965 (t80) REVERT: F 633 LYS cc_start: 0.9064 (pttp) cc_final: 0.8408 (mttp) REVERT: G 301 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7964 (t0) REVERT: G 376 PHE cc_start: 0.8078 (m-80) cc_final: 0.7766 (m-10) REVERT: G 504 ARG cc_start: 0.5981 (mtt180) cc_final: 0.4634 (mmt180) REVERT: A 82 ASN cc_start: 0.8664 (t0) cc_final: 0.8335 (t0) outliers start: 43 outliers final: 34 residues processed: 180 average time/residue: 0.1214 time to fit residues: 34.6681 Evaluate side-chains 174 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN 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 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 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 18 ARG 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 H residue 32 TYR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain I residue 88 CYS 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: 8.9990 chunk 130 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 32 optimal weight: 0.0030 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS L 6 GLN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069220 restraints weight = 56903.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.071104 restraints weight = 35037.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072398 restraints weight = 25206.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.073203 restraints weight = 20064.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073853 restraints weight = 17264.728| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18838 Z= 0.108 Angle : 0.915 43.409 25751 Z= 0.373 Chirality : 0.046 0.384 3104 Planarity : 0.004 0.054 3122 Dihedral : 5.275 81.208 2315 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 2.01 % Allowed : 9.83 % Favored : 88.17 % 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 are not related in a simple way. whole: 0.64 (0.18), residues: 2113 helix: 1.79 (0.27), residues: 396 sheet: 0.37 (0.20), residues: 574 loop : 0.05 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.011 0.001 TYR F 586 PHE 0.025 0.001 PHE E 53 TRP 0.012 0.001 TRP A 47 HIS 0.016 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (18703) covalent geometry : angle 0.89254 / 0.37 (25383) SS BOND : bond 0.00284 / 0.19 ( 37) SS BOND : angle 1.24340 / 0.93 ( 74) hydrogen bonds : bond 0.03555 / 2.36 ( 669) hydrogen bonds : angle 4.76088 / 3.33 ( 1866) link_ALPHA1-3 : bond 0.00739 / 0.38 ( 2) link_ALPHA1-3 : angle 2.05172 / 0.95 ( 6) link_BETA1-4 : bond 0.00530 / 0.35 ( 30) link_BETA1-4 : angle 1.56391 / 1.05 ( 90) link_NAG-ASN : bond 0.00391 / 0.25 ( 66) link_NAG-ASN : angle 2.23169 / 1.68 ( 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: 38 poor density : 146 time to evaluate : 0.863 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: 0.5678 (m-40) cc_final: 0.5157 (p0) REVERT: C 142 MET cc_start: 0.2702 (mmm) cc_final: 0.0581 (ttt) REVERT: D 540 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.5857 (mp-120) REVERT: D 633 LYS cc_start: 0.8970 (ptmt) cc_final: 0.8738 (pptt) REVERT: E 377 ASN cc_start: 0.8530 (t0) cc_final: 0.8288 (t0) REVERT: L 78 MET cc_start: 0.7283 (ttt) cc_final: 0.6920 (ttt) REVERT: L 97 THR cc_start: 0.8463 (m) cc_final: 0.8227 (m) REVERT: H 32 TYR cc_start: 0.5961 (OUTLIER) cc_final: 0.4664 (t80) REVERT: H 75 ARG cc_start: 0.8750 (ttm-80) cc_final: 0.8305 (mtm180) REVERT: F 633 LYS cc_start: 0.9044 (pttp) cc_final: 0.8409 (mttp) REVERT: G 301 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7951 (t0) REVERT: G 504 ARG cc_start: 0.5967 (mtt180) cc_final: 0.4654 (mmt180) REVERT: A 82 ASN cc_start: 0.8671 (t0) cc_final: 0.8339 (t0) outliers start: 38 outliers final: 26 residues processed: 175 average time/residue: 0.1198 time to fit residues: 33.2341 Evaluate side-chains 166 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 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 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL 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 301 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS 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: 4.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 422 GLN E 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.080752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.066448 restraints weight = 57536.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068219 restraints weight = 35905.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069447 restraints weight = 26093.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.070257 restraints weight = 21000.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070840 restraints weight = 18083.150| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18838 Z= 0.185 Angle : 0.972 43.504 25751 Z= 0.406 Chirality : 0.048 0.361 3104 Planarity : 0.004 0.051 3122 Dihedral : 5.537 85.124 2315 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 2.48 % Allowed : 9.61 % Favored : 87.90 % 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 are not related in a simple way. whole: 0.41 (0.18), residues: 2113 helix: 1.74 (0.27), residues: 383 sheet: 0.33 (0.21), residues: 567 loop : -0.21 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 308 TYR 0.016 0.002 TYR A 91 PHE 0.022 0.002 PHE E 53 TRP 0.014 0.001 TRP A 33 HIS 0.012 0.001 HIS L 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (18703) covalent geometry : angle 0.94745 / 0.40 (25383) SS BOND : bond 0.00363 / 0.24 ( 37) SS BOND : angle 1.31052 / 0.96 ( 74) hydrogen bonds : bond 0.04197 / 2.78 ( 669) hydrogen bonds : angle 4.95900 / 3.48 ( 1866) link_ALPHA1-3 : bond 0.00669 / 0.34 ( 2) link_ALPHA1-3 : angle 2.10918 / 0.97 ( 6) link_BETA1-4 : bond 0.00488 / 0.32 ( 30) link_BETA1-4 : angle 1.65894 / 1.10 ( 90) link_NAG-ASN : bond 0.00413 / 0.27 ( 66) link_NAG-ASN : angle 2.39147 / 1.75 ( 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 : 0.707 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: 0.5390 (m-40) cc_final: 0.5075 (p0) REVERT: D 540 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: E 307 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8607 (pt) REVERT: E 430 ILE cc_start: 0.8512 (mm) cc_final: 0.8203 (mp) REVERT: L 78 MET cc_start: 0.7280 (ttt) cc_final: 0.6883 (ttt) REVERT: H 32 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.5018 (t80) REVERT: H 75 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8409 (mtt180) REVERT: F 633 LYS cc_start: 0.9074 (pttp) cc_final: 0.8409 (mttp) REVERT: G 301 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (t0) REVERT: G 504 ARG cc_start: 0.6169 (mtt180) cc_final: 0.4726 (mmt180) REVERT: A 43 LYS cc_start: 0.7576 (mttt) cc_final: 0.7179 (pttm) REVERT: A 82 ASN cc_start: 0.8736 (t0) cc_final: 0.8397 (t0) REVERT: A 98 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7315 (p90) outliers start: 47 outliers final: 36 residues processed: 177 average time/residue: 0.1215 time to fit residues: 34.1316 Evaluate side-chains 174 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 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 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 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 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 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 G residue 301 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 98 TYR 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: 2.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.081838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.067589 restraints weight = 57388.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069419 restraints weight = 35482.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070673 restraints weight = 25592.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071524 restraints weight = 20472.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.072086 restraints weight = 17505.497| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18838 Z= 0.131 Angle : 0.940 43.429 25751 Z= 0.386 Chirality : 0.047 0.348 3104 Planarity : 0.004 0.052 3122 Dihedral : 5.419 85.923 2315 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.90 % Allowed : 10.35 % Favored : 87.74 % 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 are not related in a simple way. whole: 0.42 (0.18), residues: 2113 helix: 1.84 (0.27), residues: 384 sheet: 0.33 (0.21), residues: 568 loop : -0.22 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.014 0.001 TYR A 32 PHE 0.023 0.001 PHE E 53 TRP 0.012 0.001 TRP B 610 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (18703) covalent geometry : angle 0.91801 / 0.38 (25383) SS BOND : bond 0.00319 / 0.21 ( 37) SS BOND : angle 1.21048 / 0.90 ( 74) hydrogen bonds : bond 0.03777 / 2.51 ( 669) hydrogen bonds : angle 4.81814 / 3.37 ( 1866) link_ALPHA1-3 : bond 0.00718 / 0.37 ( 2) link_ALPHA1-3 : angle 2.10146 / 0.97 ( 6) link_BETA1-4 : bond 0.00525 / 0.34 ( 30) link_BETA1-4 : angle 1.56570 / 1.04 ( 90) link_NAG-ASN : bond 0.00386 / 0.25 ( 66) link_NAG-ASN : angle 2.22906 / 1.65 ( 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 173 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.489 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: 0.5440 (m-40) cc_final: 0.4868 (p0) REVERT: D 540 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: E 430 ILE cc_start: 0.8514 (mm) cc_final: 0.8199 (mp) REVERT: H 32 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.4903 (t80) REVERT: H 75 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8404 (mtt180) REVERT: F 633 LYS cc_start: 0.9075 (pttp) cc_final: 0.8417 (mttp) REVERT: G 301 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7983 (t0) REVERT: G 504 ARG cc_start: 0.6175 (mtt180) cc_final: 0.4810 (mmt180) REVERT: A 43 LYS cc_start: 0.7574 (mttt) cc_final: 0.7195 (pttm) REVERT: A 82 ASN cc_start: 0.8707 (t0) cc_final: 0.8354 (t0) REVERT: A 98 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7190 (p90) outliers start: 36 outliers final: 30 residues processed: 166 average time/residue: 0.1158 time to fit residues: 30.7707 Evaluate side-chains 168 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 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 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 448 ASN Chi-restraints excluded: chain L residue 3 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 75 ARG 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 I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 162 optimal weight: 2.9990 chunk 192 optimal weight: 0.0770 chunk 106 optimal weight: 0.9980 chunk 195 optimal weight: 0.0980 chunk 83 optimal weight: 0.0570 chunk 89 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069197 restraints weight = 56841.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071065 restraints weight = 34813.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072353 restraints weight = 24905.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.073222 restraints weight = 19808.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.073753 restraints weight = 16855.120| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18838 Z= 0.105 Angle : 0.917 43.385 25751 Z= 0.372 Chirality : 0.046 0.345 3104 Planarity : 0.004 0.049 3122 Dihedral : 5.240 85.581 2315 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 10.57 % Favored : 87.59 % 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 are not related in a simple way. whole: 0.57 (0.18), residues: 2113 helix: 2.10 (0.28), residues: 378 sheet: 0.43 (0.21), residues: 561 loop : -0.16 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.014 0.001 TYR B 643 PHE 0.023 0.001 PHE E 53 TRP 0.013 0.001 TRP A 47 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (18703) covalent geometry : angle 0.89816 / 0.37 (25383) SS BOND : bond 0.00272 / 0.19 ( 37) SS BOND : angle 1.14861 / 0.85 ( 74) hydrogen bonds : bond 0.03341 / 2.22 ( 669) hydrogen bonds : angle 4.64976 / 3.25 ( 1866) link_ALPHA1-3 : bond 0.00749 / 0.38 ( 2) link_ALPHA1-3 : angle 2.07598 / 0.96 ( 6) link_BETA1-4 : bond 0.00516 / 0.33 ( 30) link_BETA1-4 : angle 1.49645 / 1.00 ( 90) link_NAG-ASN : bond 0.00441 / 0.28 ( 66) link_NAG-ASN : angle 2.06200 / 1.54 ( 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 188 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5461 (m-40) cc_final: 0.5022 (p0) REVERT: C 142 MET cc_start: 0.2674 (mmm) cc_final: 0.0515 (ttt) REVERT: D 540 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.5960 (mp-120) REVERT: D 633 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8738 (pptt) REVERT: E 430 ILE cc_start: 0.8433 (mm) cc_final: 0.8129 (mp) REVERT: L 97 THR cc_start: 0.8435 (m) cc_final: 0.8203 (m) REVERT: H 32 TYR cc_start: 0.6097 (OUTLIER) cc_final: 0.4663 (t80) REVERT: H 75 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8392 (mtm180) REVERT: F 574 LYS cc_start: 0.8739 (mttt) cc_final: 0.8260 (mmtt) REVERT: F 633 LYS cc_start: 0.9040 (pttp) cc_final: 0.8414 (mttp) REVERT: G 125 LEU cc_start: 0.8950 (tp) cc_final: 0.8341 (tp) REVERT: G 301 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8045 (t0) REVERT: G 358 ILE cc_start: 0.8739 (mm) cc_final: 0.8506 (mm) REVERT: G 504 ARG cc_start: 0.6181 (mtt180) cc_final: 0.4811 (mmt180) REVERT: A 43 LYS cc_start: 0.7581 (mttt) cc_final: 0.7204 (pttm) REVERT: A 77 THR cc_start: 0.7524 (p) cc_final: 0.7106 (p) REVERT: A 82 ASN cc_start: 0.8704 (t0) cc_final: 0.8396 (t0) REVERT: A 98 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.7077 (p90) outliers start: 35 outliers final: 27 residues processed: 179 average time/residue: 0.1211 time to fit residues: 34.2531 Evaluate side-chains 179 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 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 G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 149 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 140 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.083120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068848 restraints weight = 56660.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070738 restraints weight = 34405.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072038 restraints weight = 24505.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072916 restraints weight = 19443.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073462 restraints weight = 16535.310| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18838 Z= 0.111 Angle : 0.922 43.391 25751 Z= 0.375 Chirality : 0.046 0.342 3104 Planarity : 0.004 0.051 3122 Dihedral : 5.208 85.973 2315 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.95 % Allowed : 10.62 % 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 are not related in a simple way. whole: 0.57 (0.18), residues: 2113 helix: 2.11 (0.28), residues: 378 sheet: 0.45 (0.21), residues: 561 loop : -0.19 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 308 TYR 0.012 0.001 TYR B 643 PHE 0.022 0.001 PHE E 53 TRP 0.011 0.001 TRP A 47 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (18703) covalent geometry : angle 0.90411 / 0.37 (25383) SS BOND : bond 0.00292 / 0.20 ( 37) SS BOND : angle 1.14281 / 0.85 ( 74) hydrogen bonds : bond 0.03331 / 2.20 ( 669) hydrogen bonds : angle 4.61792 / 3.24 ( 1866) link_ALPHA1-3 : bond 0.00747 / 0.38 ( 2) link_ALPHA1-3 : angle 2.08984 / 0.96 ( 6) link_BETA1-4 : bond 0.00516 / 0.34 ( 30) link_BETA1-4 : angle 1.49251 / 1.00 ( 90) link_NAG-ASN : bond 0.00396 / 0.25 ( 66) link_NAG-ASN : angle 2.05149 / 1.53 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.73 seconds wall clock time: 48 minutes 33.43 seconds (2913.43 seconds total)