Starting phenix.real_space_refine on Sun Aug 24 13:08:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl4_41361/08_2025/8tl4_41361.cif" } resolution = 3.2 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= 0.032 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 126 5.16 5 C 12546 2.51 5 N 3366 2.21 5 O 4017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20055 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.41, per 1000 atoms: 0.22 Number of scatterers: 20055 At special positions: 0 Unit cell: (154.602, 150.284, 145.965, 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 126 16.00 O 4017 8.00 N 3366 7.00 C 12546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19955 O5 NAG C 605 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Y 4 " - " MAN Y 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 88 " " NAG A 606 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN C 448 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 448 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 363 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 831.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 43 sheets defined 19.4% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.369A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.847A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.158A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 544 removed outlier: 4.076A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.143A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.725A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.018A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (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 116 removed outlier: 3.595A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.092A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.592A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.153A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 544 removed outlier: 4.096A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.112A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.682A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 639 through 663 removed outlier: 3.858A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (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 116 removed outlier: 3.578A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.820A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.149A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 removed outlier: 4.102A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.999A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.721A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.064A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.920A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.929A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.911A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.979A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.699A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.564A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.722A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.026A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.480A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.226A pdb=" N GLY B 516 " --> pdb=" O TRP G 97 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 518 " --> pdb=" O HIS G 99 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'C' and resid 495 through 499 removed outlier: 4.996A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.036A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.444A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.620A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.613A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.475A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.470A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 516 through 519 removed outlier: 6.176A pdb=" N GLY D 516 " --> pdb=" O TRP I 97 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS I 99 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 518 " --> pdb=" O HIS I 99 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.157A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.669A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.515A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 170 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.477A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.590A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.559A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 516 through 519 removed outlier: 6.191A pdb=" N GLY F 516 " --> pdb=" O TRP K 97 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS K 99 " --> pdb=" O GLY F 516 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL F 518 " --> pdb=" O HIS K 99 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN K 95 " --> pdb=" O TYR K 34 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR K 34 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.965A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.681A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.936A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.701A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.047A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.703A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6344 1.35 - 1.47: 5284 1.47 - 1.60: 8673 1.60 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 20469 Sorted by residual: bond pdb=" C ARG C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.332 1.356 -0.023 8.90e-03 1.26e+04 6.92e+00 bond pdb=" C1 NAG m 1 " pdb=" O5 NAG m 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" N GLN I 1 " pdb=" CA GLN I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 20464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 26871 1.55 - 3.11: 763 3.11 - 4.66: 146 4.66 - 6.22: 19 6.22 - 7.77: 5 Bond angle restraints: 27804 Sorted by residual: angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" N ILE B 622 " pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 111.48 108.86 2.62 9.40e-01 1.13e+00 7.76e+00 angle pdb=" N ILE D 622 " pdb=" CA ILE D 622 " pdb=" C ILE D 622 " ideal model delta sigma weight residual 111.48 108.92 2.56 9.40e-01 1.13e+00 7.42e+00 angle pdb=" N CYS C 418 " pdb=" CA CYS C 418 " pdb=" C CYS C 418 " ideal model delta sigma weight residual 108.60 112.31 -3.71 1.46e+00 4.69e-01 6.46e+00 angle pdb=" CA ASN C 136 " pdb=" CB ASN C 136 " pdb=" CG ASN C 136 " ideal model delta sigma weight residual 112.60 115.03 -2.43 1.00e+00 1.00e+00 5.92e+00 ... (remaining 27799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 12050 21.81 - 43.63: 936 43.63 - 65.44: 191 65.44 - 87.26: 52 87.26 - 109.07: 16 Dihedral angle restraints: 13245 sinusoidal: 6303 harmonic: 6942 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 2.05 -88.05 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.38 50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS C 385 " pdb=" SG CYS C 385 " pdb=" SG CYS C 418 " pdb=" CB CYS C 418 " ideal model delta sinusoidal sigma weight residual 93.00 43.30 49.70 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 13242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2861 0.060 - 0.119: 391 0.119 - 0.179: 83 0.179 - 0.238: 0 0.238 - 0.298: 7 Chirality restraints: 3342 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3339 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 88 " -0.075 2.00e-02 2.50e+03 1.03e-01 1.33e+02 pdb=" CG ASN C 88 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 88 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 88 " 0.180 2.00e-02 2.50e+03 pdb=" C1 NAG C 605 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 237 " -0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 238 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 237 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO C 238 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " 0.033 5.00e-02 4.00e+02 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 134 2.60 - 3.18: 15830 3.18 - 3.75: 28057 3.75 - 4.33: 39938 4.33 - 4.90: 68781 Nonbonded interactions: 152740 Sorted by model distance: nonbonded pdb=" OG1 THR A 139 " pdb=" OD1 ASP A 141 " model vdw 2.030 3.040 nonbonded pdb=" OG1 THR C 139 " pdb=" OD1 ASP C 141 " model vdw 2.049 3.040 nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.071 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.148 3.040 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.177 3.040 ... (remaining 152735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.900 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.004 0.038 20592 Z= 0.207 Angle : 0.698 25.329 28131 Z= 0.324 Chirality : 0.047 0.298 3342 Planarity : 0.004 0.082 3438 Dihedral : 16.040 109.070 8649 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.09 % Allowed : 16.05 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2370 helix: 2.06 (0.29), residues: 402 sheet: 0.14 (0.18), residues: 798 loop : -0.54 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 151 TYR 0.007 0.001 TYR J 36 PHE 0.012 0.001 PHE I 78 TRP 0.011 0.001 TRP G 97 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00425 (20469) covalent geometry : angle 0.63730 (27804) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.28999 ( 84) hydrogen bonds : bond 0.11382 ( 761) hydrogen bonds : angle 5.32623 ( 2067) link_ALPHA1-2 : bond 0.00317 ( 3) link_ALPHA1-2 : angle 1.72343 ( 9) link_ALPHA1-3 : bond 0.00441 ( 3) link_ALPHA1-3 : angle 1.43815 ( 9) link_BETA1-4 : bond 0.00455 ( 30) link_BETA1-4 : angle 0.92763 ( 90) link_NAG-ASN : bond 0.00393 ( 45) link_NAG-ASN : angle 3.99313 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 ARG cc_start: 0.7378 (mtp85) cc_final: 0.7149 (mtp180) REVERT: B 588 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7213 (mmm160) REVERT: B 655 LYS cc_start: 0.7795 (tptt) cc_final: 0.6954 (ttmt) REVERT: C 97 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8459 (mttp) REVERT: D 542 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7208 (mtp85) REVERT: D 588 ARG cc_start: 0.7672 (ttp-170) cc_final: 0.7059 (mmm160) REVERT: D 633 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8589 (mtmt) REVERT: E 444 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7915 (ttt-90) REVERT: E 446 VAL cc_start: 0.8752 (m) cc_final: 0.8451 (t) outliers start: 2 outliers final: 2 residues processed: 168 average time/residue: 0.1591 time to fit residues: 38.7329 Evaluate side-chains 164 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain K residue 35 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN B 607 ASN C 136 ASN C 195 ASN D 607 ASN F 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.200472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136125 restraints weight = 22704.508| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.35 r_work: 0.3080 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20592 Z= 0.164 Angle : 0.595 10.688 28131 Z= 0.295 Chirality : 0.045 0.265 3342 Planarity : 0.004 0.066 3438 Dihedral : 8.871 79.081 4266 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.75 % Allowed : 15.44 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.18), residues: 2370 helix: 2.36 (0.30), residues: 384 sheet: 0.21 (0.18), residues: 816 loop : -0.58 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 151 TYR 0.014 0.001 TYR G 90 PHE 0.021 0.002 PHE A 383 TRP 0.010 0.001 TRP A 427 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00393 (20469) covalent geometry : angle 0.56985 (27804) SS BOND : bond 0.00492 ( 42) SS BOND : angle 1.44359 ( 84) hydrogen bonds : bond 0.05021 ( 761) hydrogen bonds : angle 4.63490 ( 2067) link_ALPHA1-2 : bond 0.00692 ( 3) link_ALPHA1-2 : angle 1.69313 ( 9) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 1.55403 ( 9) link_BETA1-4 : bond 0.00856 ( 30) link_BETA1-4 : angle 1.04921 ( 90) link_NAG-ASN : bond 0.00254 ( 45) link_NAG-ASN : angle 2.14757 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 VAL cc_start: 0.8709 (m) cc_final: 0.8504 (t) REVERT: B 588 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7324 (mmm160) REVERT: B 655 LYS cc_start: 0.7792 (tptt) cc_final: 0.6862 (ttmt) REVERT: C 53 PHE cc_start: 0.8389 (p90) cc_final: 0.8184 (p90) REVERT: C 457 ASP cc_start: 0.7623 (t0) cc_final: 0.7388 (t0) REVERT: D 542 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7251 (mtp85) REVERT: D 588 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7235 (mmm160) REVERT: K 35 ASN cc_start: 0.5267 (OUTLIER) cc_final: 0.5017 (t0) REVERT: K 48 MET cc_start: 0.7447 (ptp) cc_final: 0.6765 (pmm) outliers start: 37 outliers final: 15 residues processed: 196 average time/residue: 0.1610 time to fit residues: 47.5617 Evaluate side-chains 179 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain K residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 100 optimal weight: 0.8980 chunk 214 optimal weight: 30.0000 chunk 53 optimal weight: 0.3980 chunk 175 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 200 optimal weight: 0.0050 chunk 154 optimal weight: 2.9990 chunk 188 optimal weight: 0.0870 chunk 186 optimal weight: 20.0000 overall best weight: 0.6774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN F 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.201427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.138503 restraints weight = 22922.600| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.39 r_work: 0.3048 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20592 Z= 0.114 Angle : 0.538 10.376 28131 Z= 0.268 Chirality : 0.043 0.257 3342 Planarity : 0.003 0.055 3438 Dihedral : 7.331 60.538 4265 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 16.10 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2370 helix: 2.37 (0.29), residues: 384 sheet: 0.19 (0.17), residues: 879 loop : -0.57 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 151 TYR 0.008 0.001 TYR I 91 PHE 0.017 0.001 PHE G 78 TRP 0.009 0.001 TRP E 427 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00264 (20469) covalent geometry : angle 0.50802 (27804) SS BOND : bond 0.00347 ( 42) SS BOND : angle 1.35755 ( 84) hydrogen bonds : bond 0.04243 ( 761) hydrogen bonds : angle 4.44946 ( 2067) link_ALPHA1-2 : bond 0.00527 ( 3) link_ALPHA1-2 : angle 1.54280 ( 9) link_ALPHA1-3 : bond 0.01247 ( 3) link_ALPHA1-3 : angle 1.35778 ( 9) link_BETA1-4 : bond 0.00570 ( 30) link_BETA1-4 : angle 1.08606 ( 90) link_NAG-ASN : bond 0.00258 ( 45) link_NAG-ASN : angle 2.21894 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7915 (mmm) cc_final: 0.7663 (tpt) REVERT: A 446 VAL cc_start: 0.8675 (m) cc_final: 0.8471 (t) REVERT: A 457 ASP cc_start: 0.7844 (t0) cc_final: 0.7565 (t0) REVERT: B 588 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.7316 (mmm160) REVERT: B 655 LYS cc_start: 0.7764 (tptt) cc_final: 0.6714 (mtmt) REVERT: C 457 ASP cc_start: 0.7612 (t0) cc_final: 0.7335 (t0) REVERT: D 540 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: D 542 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7192 (mtp85) REVERT: D 588 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7252 (mmm160) REVERT: F 540 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7778 (mp-120) REVERT: G 48 MET cc_start: 0.7074 (ptp) cc_final: 0.6654 (pmm) REVERT: I 48 MET cc_start: 0.7349 (ptp) cc_final: 0.6686 (pmm) REVERT: K 35 ASN cc_start: 0.5322 (OUTLIER) cc_final: 0.5101 (t0) REVERT: K 48 MET cc_start: 0.7505 (ptp) cc_final: 0.6811 (pmm) outliers start: 42 outliers final: 22 residues processed: 191 average time/residue: 0.1581 time to fit residues: 45.2784 Evaluate side-chains 183 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 95 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 30.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN F 607 ASN I 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.199503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138464 restraints weight = 22678.393| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.53 r_work: 0.2889 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20592 Z= 0.190 Angle : 0.634 11.984 28131 Z= 0.311 Chirality : 0.046 0.261 3342 Planarity : 0.004 0.051 3438 Dihedral : 6.393 49.719 4265 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.88 % Allowed : 16.10 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2370 helix: 2.01 (0.29), residues: 384 sheet: 0.21 (0.17), residues: 873 loop : -0.65 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.010 0.001 TYR A 486 PHE 0.024 0.002 PHE E 383 TRP 0.012 0.001 TRP A 427 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00472 (20469) covalent geometry : angle 0.60059 (27804) SS BOND : bond 0.00470 ( 42) SS BOND : angle 1.85937 ( 84) hydrogen bonds : bond 0.05495 ( 761) hydrogen bonds : angle 4.58229 ( 2067) link_ALPHA1-2 : bond 0.00401 ( 3) link_ALPHA1-2 : angle 1.54727 ( 9) link_ALPHA1-3 : bond 0.01073 ( 3) link_ALPHA1-3 : angle 1.34360 ( 9) link_BETA1-4 : bond 0.00589 ( 30) link_BETA1-4 : angle 1.29952 ( 90) link_NAG-ASN : bond 0.00227 ( 45) link_NAG-ASN : angle 2.42339 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9137 (p) cc_final: 0.8898 (t) REVERT: A 446 VAL cc_start: 0.8755 (m) cc_final: 0.8482 (t) REVERT: A 457 ASP cc_start: 0.7885 (t0) cc_final: 0.7618 (t0) REVERT: B 588 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.7407 (mmm160) REVERT: B 655 LYS cc_start: 0.7777 (tptt) cc_final: 0.6709 (mtmt) REVERT: C 457 ASP cc_start: 0.7708 (t0) cc_final: 0.7397 (t0) REVERT: D 542 ARG cc_start: 0.7749 (mtm-85) cc_final: 0.7182 (mtp85) REVERT: D 588 ARG cc_start: 0.8384 (ttp-170) cc_final: 0.7284 (mmm160) REVERT: E 151 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: G 48 MET cc_start: 0.7329 (ptp) cc_final: 0.6758 (pmm) REVERT: G 80 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.3676 (mm) REVERT: I 35 ASN cc_start: 0.5796 (OUTLIER) cc_final: 0.5322 (t0) REVERT: K 80 LEU cc_start: 0.4882 (OUTLIER) cc_final: 0.3632 (mm) outliers start: 61 outliers final: 35 residues processed: 208 average time/residue: 0.1425 time to fit residues: 45.2214 Evaluate side-chains 195 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 189 optimal weight: 30.0000 chunk 200 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN F 607 ASN F 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.199242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144347 restraints weight = 22654.535| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.34 r_work: 0.2921 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20592 Z= 0.192 Angle : 0.629 9.856 28131 Z= 0.309 Chirality : 0.046 0.264 3342 Planarity : 0.004 0.048 3438 Dihedral : 5.772 53.942 4265 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.54 % Allowed : 16.24 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.17), residues: 2370 helix: 1.35 (0.28), residues: 420 sheet: 0.35 (0.17), residues: 840 loop : -0.82 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 38 TYR 0.010 0.001 TYR E 384 PHE 0.024 0.002 PHE E 383 TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00476 (20469) covalent geometry : angle 0.59340 (27804) SS BOND : bond 0.00475 ( 42) SS BOND : angle 1.85199 ( 84) hydrogen bonds : bond 0.05355 ( 761) hydrogen bonds : angle 4.58544 ( 2067) link_ALPHA1-2 : bond 0.00294 ( 3) link_ALPHA1-2 : angle 1.64001 ( 9) link_ALPHA1-3 : bond 0.01114 ( 3) link_ALPHA1-3 : angle 1.29363 ( 9) link_BETA1-4 : bond 0.00586 ( 30) link_BETA1-4 : angle 1.31394 ( 90) link_NAG-ASN : bond 0.00217 ( 45) link_NAG-ASN : angle 2.52091 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 167 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9130 (p) cc_final: 0.8880 (t) REVERT: A 72 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: A 446 VAL cc_start: 0.8730 (m) cc_final: 0.8427 (t) REVERT: A 457 ASP cc_start: 0.7872 (t0) cc_final: 0.7570 (t0) REVERT: B 539 VAL cc_start: 0.8688 (p) cc_final: 0.8483 (m) REVERT: B 588 ARG cc_start: 0.8386 (ttp-170) cc_final: 0.7355 (mmm160) REVERT: B 655 LYS cc_start: 0.7803 (tptt) cc_final: 0.6697 (mtmt) REVERT: C 457 ASP cc_start: 0.7693 (t0) cc_final: 0.7465 (t0) REVERT: D 540 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7661 (mp-120) REVERT: D 542 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7205 (mtp85) REVERT: D 588 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.7220 (mmm160) REVERT: F 617 ARG cc_start: 0.7304 (mtp85) cc_final: 0.7073 (mtp85) REVERT: G 48 MET cc_start: 0.7307 (ptp) cc_final: 0.6657 (pmm) REVERT: G 80 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.3590 (mm) REVERT: I 35 ASN cc_start: 0.5809 (OUTLIER) cc_final: 0.5328 (t0) REVERT: K 80 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.3646 (mm) outliers start: 75 outliers final: 45 residues processed: 226 average time/residue: 0.1411 time to fit residues: 49.2785 Evaluate side-chains 216 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.201557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151162 restraints weight = 22545.655| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.09 r_work: 0.2879 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20592 Z= 0.113 Angle : 0.562 10.493 28131 Z= 0.277 Chirality : 0.043 0.260 3342 Planarity : 0.003 0.043 3438 Dihedral : 5.333 54.939 4265 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.83 % Allowed : 17.52 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 2370 helix: 1.88 (0.29), residues: 402 sheet: 0.32 (0.17), residues: 873 loop : -0.69 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 151 TYR 0.009 0.001 TYR A 173 PHE 0.017 0.001 PHE C 383 TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00260 (20469) covalent geometry : angle 0.52652 (27804) SS BOND : bond 0.00404 ( 42) SS BOND : angle 1.70307 ( 84) hydrogen bonds : bond 0.04369 ( 761) hydrogen bonds : angle 4.40347 ( 2067) link_ALPHA1-2 : bond 0.00299 ( 3) link_ALPHA1-2 : angle 1.70165 ( 9) link_ALPHA1-3 : bond 0.01155 ( 3) link_ALPHA1-3 : angle 1.28415 ( 9) link_BETA1-4 : bond 0.00553 ( 30) link_BETA1-4 : angle 1.21274 ( 90) link_NAG-ASN : bond 0.00264 ( 45) link_NAG-ASN : angle 2.36447 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.5693 (t-90) REVERT: A 446 VAL cc_start: 0.8687 (m) cc_final: 0.8431 (t) REVERT: A 457 ASP cc_start: 0.7685 (t0) cc_final: 0.7387 (t0) REVERT: B 539 VAL cc_start: 0.8783 (p) cc_final: 0.8573 (m) REVERT: B 588 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.7523 (mmm160) REVERT: B 655 LYS cc_start: 0.7919 (tptt) cc_final: 0.6817 (mtmt) REVERT: C 457 ASP cc_start: 0.7644 (t0) cc_final: 0.7303 (t0) REVERT: D 540 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7862 (mp-120) REVERT: D 542 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7225 (mtp85) REVERT: D 588 ARG cc_start: 0.8443 (ttp-170) cc_final: 0.7468 (mmm160) REVERT: E 232 LYS cc_start: 0.8303 (mmmm) cc_final: 0.8011 (mmtm) REVERT: F 617 ARG cc_start: 0.7412 (mtp85) cc_final: 0.7203 (mtp85) REVERT: G 48 MET cc_start: 0.7405 (ptp) cc_final: 0.6764 (pmm) REVERT: G 80 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.3638 (mm) REVERT: I 35 ASN cc_start: 0.5845 (OUTLIER) cc_final: 0.5347 (t0) REVERT: K 80 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.3839 (mm) REVERT: L 31 THR cc_start: 0.5419 (OUTLIER) cc_final: 0.5144 (p) outliers start: 60 outliers final: 33 residues processed: 216 average time/residue: 0.1624 time to fit residues: 52.7968 Evaluate side-chains 202 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 35 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN C 348 GLN E 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.199108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140781 restraints weight = 22543.451| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.32 r_work: 0.2925 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20592 Z= 0.148 Angle : 0.586 12.832 28131 Z= 0.289 Chirality : 0.044 0.263 3342 Planarity : 0.003 0.041 3438 Dihedral : 5.203 55.014 4263 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.21 % Allowed : 16.95 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 2370 helix: 1.82 (0.29), residues: 402 sheet: 0.36 (0.17), residues: 867 loop : -0.69 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 444 TYR 0.007 0.001 TYR E 384 PHE 0.020 0.002 PHE E 383 TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00361 (20469) covalent geometry : angle 0.55216 (27804) SS BOND : bond 0.00461 ( 42) SS BOND : angle 1.77409 ( 84) hydrogen bonds : bond 0.04690 ( 761) hydrogen bonds : angle 4.42336 ( 2067) link_ALPHA1-2 : bond 0.00300 ( 3) link_ALPHA1-2 : angle 1.65628 ( 9) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.23541 ( 9) link_BETA1-4 : bond 0.00557 ( 30) link_BETA1-4 : angle 1.23174 ( 90) link_NAG-ASN : bond 0.00245 ( 45) link_NAG-ASN : angle 2.37006 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 166 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.5562 (t-90) REVERT: A 446 VAL cc_start: 0.8691 (m) cc_final: 0.8414 (t) REVERT: A 457 ASP cc_start: 0.7821 (t0) cc_final: 0.7496 (t0) REVERT: B 539 VAL cc_start: 0.8722 (p) cc_final: 0.8502 (m) REVERT: B 588 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7364 (mmm160) REVERT: B 655 LYS cc_start: 0.7710 (tptt) cc_final: 0.6581 (mtmt) REVERT: C 348 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6975 (mp-120) REVERT: C 457 ASP cc_start: 0.7700 (t0) cc_final: 0.7345 (t0) REVERT: D 540 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7653 (mp-120) REVERT: D 542 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7145 (mtp85) REVERT: D 588 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.7250 (mmm160) REVERT: G 80 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.3587 (mm) REVERT: I 35 ASN cc_start: 0.5834 (OUTLIER) cc_final: 0.5335 (t0) REVERT: K 80 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.3807 (mm) outliers start: 68 outliers final: 43 residues processed: 223 average time/residue: 0.1546 time to fit residues: 52.6809 Evaluate side-chains 213 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 355 ASN C 114 GLN C 348 GLN E 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.200256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143557 restraints weight = 22655.302| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.39 r_work: 0.2962 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20592 Z= 0.129 Angle : 0.576 12.051 28131 Z= 0.284 Chirality : 0.043 0.262 3342 Planarity : 0.003 0.040 3438 Dihedral : 5.051 55.706 4263 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.83 % Allowed : 17.47 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.18), residues: 2370 helix: 1.87 (0.29), residues: 402 sheet: 0.39 (0.17), residues: 867 loop : -0.68 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 444 TYR 0.007 0.001 TYR A 173 PHE 0.018 0.001 PHE E 383 TRP 0.011 0.001 TRP E 427 HIS 0.003 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00307 (20469) covalent geometry : angle 0.54181 (27804) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.71684 ( 84) hydrogen bonds : bond 0.04469 ( 761) hydrogen bonds : angle 4.37539 ( 2067) link_ALPHA1-2 : bond 0.00308 ( 3) link_ALPHA1-2 : angle 1.67957 ( 9) link_ALPHA1-3 : bond 0.01052 ( 3) link_ALPHA1-3 : angle 1.17624 ( 9) link_BETA1-4 : bond 0.00543 ( 30) link_BETA1-4 : angle 1.21019 ( 90) link_NAG-ASN : bond 0.00283 ( 45) link_NAG-ASN : angle 2.36579 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5882 (OUTLIER) cc_final: 0.5578 (t-90) REVERT: A 446 VAL cc_start: 0.8684 (m) cc_final: 0.8410 (t) REVERT: A 457 ASP cc_start: 0.7732 (t0) cc_final: 0.7400 (t0) REVERT: B 539 VAL cc_start: 0.8724 (p) cc_final: 0.8511 (m) REVERT: B 542 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7218 (mtm-85) REVERT: B 588 ARG cc_start: 0.8382 (ttp-170) cc_final: 0.7365 (mmm160) REVERT: B 655 LYS cc_start: 0.7722 (tptt) cc_final: 0.6586 (mtmt) REVERT: C 348 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6583 (mp-120) REVERT: C 457 ASP cc_start: 0.7685 (t0) cc_final: 0.7334 (t0) REVERT: D 540 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7736 (mp-120) REVERT: D 542 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7136 (mtp85) REVERT: D 588 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.7303 (mmm160) REVERT: E 232 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7700 (mmtm) REVERT: E 500 ARG cc_start: 0.7511 (mtt90) cc_final: 0.7293 (mtt-85) REVERT: G 48 MET cc_start: 0.7320 (ptp) cc_final: 0.6691 (pmm) REVERT: G 80 LEU cc_start: 0.4848 (OUTLIER) cc_final: 0.3635 (mm) REVERT: I 35 ASN cc_start: 0.5819 (OUTLIER) cc_final: 0.5334 (t0) REVERT: K 35 ASN cc_start: 0.5598 (OUTLIER) cc_final: 0.5155 (t0) REVERT: K 80 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.3794 (mm) REVERT: L 31 THR cc_start: 0.5626 (OUTLIER) cc_final: 0.5372 (p) outliers start: 60 outliers final: 46 residues processed: 215 average time/residue: 0.1673 time to fit residues: 53.6697 Evaluate side-chains 219 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 355 ASN C 137 ASN C 348 GLN E 136 ASN K 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.199584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143317 restraints weight = 22467.757| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.39 r_work: 0.2893 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20592 Z= 0.188 Angle : 0.629 12.874 28131 Z= 0.309 Chirality : 0.046 0.265 3342 Planarity : 0.004 0.063 3438 Dihedral : 5.141 57.085 4263 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.93 % Allowed : 17.33 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.18), residues: 2370 helix: 1.67 (0.29), residues: 402 sheet: 0.36 (0.17), residues: 867 loop : -0.73 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 444 TYR 0.009 0.001 TYR E 384 PHE 0.024 0.002 PHE E 383 TRP 0.012 0.001 TRP C 427 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00468 (20469) covalent geometry : angle 0.59471 (27804) SS BOND : bond 0.00503 ( 42) SS BOND : angle 1.90135 ( 84) hydrogen bonds : bond 0.05136 ( 761) hydrogen bonds : angle 4.47242 ( 2067) link_ALPHA1-2 : bond 0.00281 ( 3) link_ALPHA1-2 : angle 1.65040 ( 9) link_ALPHA1-3 : bond 0.00989 ( 3) link_ALPHA1-3 : angle 1.17187 ( 9) link_BETA1-4 : bond 0.00565 ( 30) link_BETA1-4 : angle 1.27758 ( 90) link_NAG-ASN : bond 0.00266 ( 45) link_NAG-ASN : angle 2.42136 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5881 (OUTLIER) cc_final: 0.5451 (m90) REVERT: A 446 VAL cc_start: 0.8751 (m) cc_final: 0.8460 (t) REVERT: A 457 ASP cc_start: 0.7847 (t0) cc_final: 0.7514 (t0) REVERT: A 500 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.7521 (mtt-85) REVERT: B 539 VAL cc_start: 0.8732 (p) cc_final: 0.8515 (m) REVERT: B 588 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7393 (mmm160) REVERT: B 655 LYS cc_start: 0.7798 (tptt) cc_final: 0.6688 (mtmt) REVERT: C 348 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6599 (mp-120) REVERT: C 457 ASP cc_start: 0.7739 (t0) cc_final: 0.7494 (t0) REVERT: D 542 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7131 (mtp85) REVERT: D 588 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7279 (mmm160) REVERT: E 500 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7331 (mtt-85) REVERT: G 48 MET cc_start: 0.7307 (ptp) cc_final: 0.6677 (pmm) REVERT: G 80 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.3714 (mm) REVERT: I 35 ASN cc_start: 0.5875 (OUTLIER) cc_final: 0.5331 (t0) REVERT: K 35 ASN cc_start: 0.5615 (OUTLIER) cc_final: 0.5142 (t0) REVERT: K 80 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.3812 (mm) REVERT: L 31 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5262 (p) outliers start: 62 outliers final: 45 residues processed: 222 average time/residue: 0.1648 time to fit residues: 55.4425 Evaluate side-chains 223 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 165 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 137 ASN C 348 GLN E 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.199382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142172 restraints weight = 22656.754| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.40 r_work: 0.2905 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20592 Z= 0.187 Angle : 0.636 12.885 28131 Z= 0.312 Chirality : 0.046 0.265 3342 Planarity : 0.004 0.075 3438 Dihedral : 5.195 59.855 4263 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.79 % Allowed : 17.42 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.17), residues: 2370 helix: 1.35 (0.28), residues: 420 sheet: 0.44 (0.18), residues: 840 loop : -0.85 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 444 TYR 0.009 0.001 TYR E 384 PHE 0.024 0.002 PHE E 383 TRP 0.012 0.001 TRP C 427 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00465 (20469) covalent geometry : angle 0.60092 (27804) SS BOND : bond 0.00490 ( 42) SS BOND : angle 2.00025 ( 84) hydrogen bonds : bond 0.05194 ( 761) hydrogen bonds : angle 4.48681 ( 2067) link_ALPHA1-2 : bond 0.00255 ( 3) link_ALPHA1-2 : angle 1.68172 ( 9) link_ALPHA1-3 : bond 0.01024 ( 3) link_ALPHA1-3 : angle 1.18064 ( 9) link_BETA1-4 : bond 0.00561 ( 30) link_BETA1-4 : angle 1.29799 ( 90) link_NAG-ASN : bond 0.00250 ( 45) link_NAG-ASN : angle 2.46739 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.5904 (OUTLIER) cc_final: 0.5445 (m90) REVERT: A 446 VAL cc_start: 0.8729 (m) cc_final: 0.8428 (t) REVERT: A 457 ASP cc_start: 0.7846 (t0) cc_final: 0.7511 (t0) REVERT: A 500 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7539 (mtt-85) REVERT: B 539 VAL cc_start: 0.8689 (p) cc_final: 0.8463 (m) REVERT: B 588 ARG cc_start: 0.8351 (ttp-170) cc_final: 0.7288 (mmm160) REVERT: B 655 LYS cc_start: 0.7713 (tptt) cc_final: 0.6593 (mtmt) REVERT: C 129 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 348 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6632 (mp-120) REVERT: C 457 ASP cc_start: 0.7756 (t0) cc_final: 0.7509 (t0) REVERT: D 542 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7099 (mtp85) REVERT: D 588 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.7167 (mmm160) REVERT: E 232 LYS cc_start: 0.8131 (mtmm) cc_final: 0.7689 (mmtm) REVERT: E 500 ARG cc_start: 0.7536 (mtt90) cc_final: 0.7304 (mtt-85) REVERT: G 48 MET cc_start: 0.7296 (ptp) cc_final: 0.6676 (pmm) REVERT: G 80 LEU cc_start: 0.4945 (OUTLIER) cc_final: 0.3709 (mm) REVERT: I 35 ASN cc_start: 0.5855 (OUTLIER) cc_final: 0.5323 (t0) REVERT: K 35 ASN cc_start: 0.5647 (OUTLIER) cc_final: 0.5178 (t0) REVERT: K 80 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.3843 (mm) REVERT: L 31 THR cc_start: 0.5552 (OUTLIER) cc_final: 0.5339 (p) outliers start: 59 outliers final: 47 residues processed: 219 average time/residue: 0.1684 time to fit residues: 55.9272 Evaluate side-chains 225 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 154 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 189 optimal weight: 40.0000 chunk 230 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 137 ASN C 348 GLN E 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.200483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143110 restraints weight = 22696.711| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.31 r_work: 0.2968 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20592 Z= 0.141 Angle : 0.589 12.164 28131 Z= 0.292 Chirality : 0.044 0.262 3342 Planarity : 0.004 0.067 3438 Dihedral : 5.054 58.146 4263 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.79 % Allowed : 17.37 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.18), residues: 2370 helix: 1.74 (0.29), residues: 402 sheet: 0.38 (0.17), residues: 867 loop : -0.73 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 444 TYR 0.007 0.001 TYR A 173 PHE 0.019 0.001 PHE E 383 TRP 0.012 0.001 TRP C 427 HIS 0.003 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00338 (20469) covalent geometry : angle 0.55412 (27804) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.79326 ( 84) hydrogen bonds : bond 0.04711 ( 761) hydrogen bonds : angle 4.41485 ( 2067) link_ALPHA1-2 : bond 0.00254 ( 3) link_ALPHA1-2 : angle 1.70424 ( 9) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 1.11229 ( 9) link_BETA1-4 : bond 0.00539 ( 30) link_BETA1-4 : angle 1.25318 ( 90) link_NAG-ASN : bond 0.00245 ( 45) link_NAG-ASN : angle 2.41648 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6345.71 seconds wall clock time: 109 minutes 2.13 seconds (6542.13 seconds total)