Starting phenix.real_space_refine on Tue May 20 14:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl4_41361/05_2025/8tl4_41361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl4_41361/05_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_41361/05_2025/8tl4_41361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl4_41361/05_2025/8tl4_41361.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl4_41361/05_2025/8tl4_41361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl4_41361/05_2025/8tl4_41361.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.69, per 1000 atoms: 0.63 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: 4.99 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.55 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: 7.27 Time building geometry restraints manager: 5.83 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.740 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.140 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP G 97 HIS 0.004 0.001 HIS C 216 PHE 0.012 0.001 PHE I 78 TYR 0.007 0.001 TYR J 36 ARG 0.010 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 45) link_NAG-ASN : angle 3.99313 ( 135) link_BETA1-4 : bond 0.00455 ( 30) link_BETA1-4 : angle 0.92763 ( 90) 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) hydrogen bonds : bond 0.11382 ( 761) hydrogen bonds : angle 5.32623 ( 2067) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.28999 ( 84) covalent geometry : bond 0.00425 (20469) covalent geometry : angle 0.63730 (27804) *********************** 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 : 1.958 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: 0.3698 time to fit residues: 90.3744 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 : 1.973 ------------------------------------------------------------------------------- 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 202 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- 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 B 607 ASN C 136 ASN C 195 ASN D 607 ASN F 607 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.203535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143817 restraints weight = 22826.130| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.32 r_work: 0.3083 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20592 Z= 0.134 Angle : 0.567 9.432 28131 Z= 0.282 Chirality : 0.043 0.259 3342 Planarity : 0.004 0.063 3438 Dihedral : 8.732 77.582 4266 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.75 % Allowed : 15.11 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2370 helix: 2.45 (0.30), residues: 384 sheet: 0.19 (0.17), residues: 822 loop : -0.57 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 96 HIS 0.004 0.001 HIS C 374 PHE 0.017 0.002 PHE A 383 TYR 0.015 0.001 TYR G 90 ARG 0.005 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 45) link_NAG-ASN : angle 2.09509 ( 135) link_BETA1-4 : bond 0.00688 ( 30) link_BETA1-4 : angle 1.03971 ( 90) link_ALPHA1-2 : bond 0.00690 ( 3) link_ALPHA1-2 : angle 1.61619 ( 9) link_ALPHA1-3 : bond 0.01294 ( 3) link_ALPHA1-3 : angle 1.71300 ( 9) hydrogen bonds : bond 0.04426 ( 761) hydrogen bonds : angle 4.55533 ( 2067) SS BOND : bond 0.00366 ( 42) SS BOND : angle 1.26552 ( 84) covalent geometry : bond 0.00315 (20469) covalent geometry : angle 0.54176 (27804) *********************** 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 209 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7700 (t0) cc_final: 0.7334 (t0) REVERT: B 588 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7233 (mmm160) REVERT: B 655 LYS cc_start: 0.7713 (tptt) cc_final: 0.6764 (ttmt) REVERT: C 457 ASP cc_start: 0.7604 (t0) cc_final: 0.7366 (t0) REVERT: D 542 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7214 (mtp85) REVERT: D 588 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7155 (mmm160) REVERT: K 48 MET cc_start: 0.7411 (ptp) cc_final: 0.6728 (pmm) outliers start: 37 outliers final: 14 residues processed: 197 average time/residue: 0.3530 time to fit residues: 105.0481 Evaluate side-chains 175 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 229 optimal weight: 40.0000 chunk 92 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 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 A 328 GLN C 136 ASN F 607 ASN I 81 HIS K 35AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.199726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136846 restraints weight = 22773.992| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.39 r_work: 0.2966 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20592 Z= 0.139 Angle : 0.569 11.146 28131 Z= 0.282 Chirality : 0.044 0.256 3342 Planarity : 0.003 0.053 3438 Dihedral : 7.183 58.690 4263 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.89 % Allowed : 16.10 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.18), residues: 2370 helix: 2.28 (0.29), residues: 384 sheet: 0.22 (0.17), residues: 873 loop : -0.56 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.003 0.001 HIS C 374 PHE 0.019 0.002 PHE A 383 TYR 0.008 0.001 TYR A 486 ARG 0.005 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 45) link_NAG-ASN : angle 2.25526 ( 135) link_BETA1-4 : bond 0.00572 ( 30) link_BETA1-4 : angle 1.14155 ( 90) link_ALPHA1-2 : bond 0.00509 ( 3) link_ALPHA1-2 : angle 1.50074 ( 9) link_ALPHA1-3 : bond 0.01202 ( 3) link_ALPHA1-3 : angle 1.26543 ( 9) hydrogen bonds : bond 0.04642 ( 761) hydrogen bonds : angle 4.50847 ( 2067) SS BOND : bond 0.00387 ( 42) SS BOND : angle 1.53024 ( 84) covalent geometry : bond 0.00335 (20469) covalent geometry : angle 0.53930 (27804) *********************** 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 204 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7797 (t0) cc_final: 0.7412 (t0) REVERT: B 542 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7026 (mtm-85) REVERT: B 588 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.7259 (mmm160) REVERT: B 655 LYS cc_start: 0.7687 (tptt) cc_final: 0.6632 (mtmt) REVERT: C 457 ASP cc_start: 0.7632 (t0) cc_final: 0.7345 (t0) REVERT: D 540 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7679 (mp-120) REVERT: D 542 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7157 (mtp85) REVERT: D 588 ARG cc_start: 0.8251 (ttp-170) cc_final: 0.7194 (mmm160) REVERT: F 536 THR cc_start: 0.8519 (p) cc_final: 0.7598 (p) REVERT: F 540 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7776 (mp-120) REVERT: G 48 MET cc_start: 0.7031 (ptp) cc_final: 0.6646 (pmm) REVERT: I 48 MET cc_start: 0.7460 (ptp) cc_final: 0.6690 (pmm) outliers start: 40 outliers final: 19 residues processed: 194 average time/residue: 0.3626 time to fit residues: 105.9232 Evaluate side-chains 180 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 499 THR 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 616 ASN Chi-restraints excluded: chain E residue 134 VAL 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 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 218 optimal weight: 30.0000 chunk 215 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 155 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 114 GLN C 136 ASN E 136 ASN F 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.198329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135207 restraints weight = 22775.074| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.44 r_work: 0.2873 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20592 Z= 0.235 Angle : 0.689 12.165 28131 Z= 0.337 Chirality : 0.048 0.262 3342 Planarity : 0.004 0.048 3438 Dihedral : 6.465 50.959 4263 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.26 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2370 helix: 1.71 (0.29), residues: 387 sheet: 0.17 (0.17), residues: 873 loop : -0.74 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.004 0.001 HIS G 99 PHE 0.027 0.002 PHE E 383 TYR 0.011 0.001 TYR A 486 ARG 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 45) link_NAG-ASN : angle 2.55945 ( 135) link_BETA1-4 : bond 0.00615 ( 30) link_BETA1-4 : angle 1.40204 ( 90) link_ALPHA1-2 : bond 0.00358 ( 3) link_ALPHA1-2 : angle 1.52461 ( 9) link_ALPHA1-3 : bond 0.01071 ( 3) link_ALPHA1-3 : angle 1.35741 ( 9) hydrogen bonds : bond 0.06087 ( 761) hydrogen bonds : angle 4.70094 ( 2067) SS BOND : bond 0.00490 ( 42) SS BOND : angle 1.93819 ( 84) covalent geometry : bond 0.00590 (20469) covalent geometry : angle 0.65563 (27804) *********************** 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 236 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 1.874 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: 0.9136 (p) cc_final: 0.8879 (t) REVERT: A 457 ASP cc_start: 0.7846 (t0) cc_final: 0.7479 (t0) REVERT: B 588 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.7367 (mmm160) REVERT: B 655 LYS cc_start: 0.7775 (tptt) cc_final: 0.6682 (mtmt) REVERT: D 542 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7202 (mtp85) REVERT: D 588 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.7282 (mmm160) REVERT: E 321 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: G 48 MET cc_start: 0.7337 (ptp) cc_final: 0.6691 (pmm) REVERT: G 80 LEU cc_start: 0.4847 (OUTLIER) cc_final: 0.3624 (mm) REVERT: I 35 ASN cc_start: 0.5826 (OUTLIER) cc_final: 0.5310 (t0) REVERT: K 80 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.3700 (mm) outliers start: 69 outliers final: 34 residues processed: 223 average time/residue: 0.3170 time to fit residues: 109.5195 Evaluate side-chains 198 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.944 ------------------------------------------------------------------------------- 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 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 202 THR 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 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 321 ASP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 612 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 90 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 206 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.201784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139705 restraints weight = 22718.450| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.43 r_work: 0.2957 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20592 Z= 0.119 Angle : 0.564 11.226 28131 Z= 0.278 Chirality : 0.043 0.258 3342 Planarity : 0.003 0.042 3438 Dihedral : 5.596 53.337 4263 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.64 % Allowed : 17.00 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2370 helix: 1.57 (0.28), residues: 420 sheet: 0.35 (0.17), residues: 852 loop : -0.75 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 PHE 0.017 0.001 PHE C 383 TYR 0.009 0.001 TYR A 173 ARG 0.004 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 45) link_NAG-ASN : angle 2.36989 ( 135) link_BETA1-4 : bond 0.00568 ( 30) link_BETA1-4 : angle 1.20343 ( 90) link_ALPHA1-2 : bond 0.00332 ( 3) link_ALPHA1-2 : angle 1.64746 ( 9) link_ALPHA1-3 : bond 0.01214 ( 3) link_ALPHA1-3 : angle 1.28721 ( 9) hydrogen bonds : bond 0.04378 ( 761) hydrogen bonds : angle 4.44719 ( 2067) SS BOND : bond 0.00414 ( 42) SS BOND : angle 1.58646 ( 84) covalent geometry : bond 0.00274 (20469) covalent geometry : angle 0.52954 (27804) *********************** 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 218 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 162 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7786 (t0) cc_final: 0.7419 (t0) REVERT: B 588 ARG cc_start: 0.8338 (ttp-170) cc_final: 0.7346 (mmm160) REVERT: B 655 LYS cc_start: 0.7705 (tptt) cc_final: 0.6604 (mtmt) REVERT: C 457 ASP cc_start: 0.7787 (t0) cc_final: 0.7578 (t0) REVERT: D 540 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7740 (mp-120) REVERT: D 542 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7155 (mtp85) REVERT: D 588 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.7256 (mmm160) REVERT: G 48 MET cc_start: 0.7358 (ptp) cc_final: 0.6712 (pmm) REVERT: G 80 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.3608 (mm) REVERT: I 35 ASN cc_start: 0.5737 (OUTLIER) cc_final: 0.5337 (t0) REVERT: K 80 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.3730 (mm) outliers start: 56 outliers final: 33 residues processed: 207 average time/residue: 0.3427 time to fit residues: 106.9872 Evaluate side-chains 194 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP 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 184 ILE Chi-restraints excluded: chain C residue 194 ILE 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 433 CYS 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 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 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 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 58 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.202428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145946 restraints weight = 22824.699| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.29 r_work: 0.3074 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20592 Z= 0.111 Angle : 0.547 10.989 28131 Z= 0.270 Chirality : 0.043 0.263 3342 Planarity : 0.003 0.040 3438 Dihedral : 5.030 50.825 4263 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.69 % Allowed : 17.14 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2370 helix: 2.00 (0.29), residues: 402 sheet: 0.36 (0.17), residues: 873 loop : -0.66 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.003 0.001 HIS I 77 PHE 0.015 0.001 PHE E 383 TYR 0.008 0.001 TYR A 173 ARG 0.004 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 45) link_NAG-ASN : angle 2.24343 ( 135) link_BETA1-4 : bond 0.00533 ( 30) link_BETA1-4 : angle 1.16599 ( 90) link_ALPHA1-2 : bond 0.00352 ( 3) link_ALPHA1-2 : angle 1.64523 ( 9) link_ALPHA1-3 : bond 0.01114 ( 3) link_ALPHA1-3 : angle 1.28131 ( 9) hydrogen bonds : bond 0.04094 ( 761) hydrogen bonds : angle 4.34441 ( 2067) SS BOND : bond 0.00432 ( 42) SS BOND : angle 1.56183 ( 84) covalent geometry : bond 0.00254 (20469) covalent geometry : angle 0.51491 (27804) *********************** 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 219 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7651 (t0) cc_final: 0.7281 (t0) REVERT: B 588 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7320 (mmm160) REVERT: B 655 LYS cc_start: 0.7711 (tptt) cc_final: 0.6595 (mtmt) REVERT: C 97 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8141 (mttp) REVERT: C 457 ASP cc_start: 0.7741 (t0) cc_final: 0.7474 (t0) REVERT: D 540 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7731 (mp-120) REVERT: D 542 ARG cc_start: 0.7665 (mtm-85) cc_final: 0.7126 (mtp85) REVERT: D 588 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.7247 (mmm160) REVERT: E 232 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7901 (mmtm) REVERT: F 536 THR cc_start: 0.8488 (p) cc_final: 0.7593 (p) REVERT: F 540 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7731 (mp-120) REVERT: G 48 MET cc_start: 0.7305 (ptp) cc_final: 0.6656 (pmm) REVERT: G 80 LEU cc_start: 0.4815 (OUTLIER) cc_final: 0.3592 (mm) REVERT: I 35 ASN cc_start: 0.5731 (OUTLIER) cc_final: 0.5320 (t0) REVERT: K 48 MET cc_start: 0.7419 (ptp) cc_final: 0.7210 (ptp) REVERT: K 80 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.3748 (mm) REVERT: L 31 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5423 (p) outliers start: 57 outliers final: 38 residues processed: 205 average time/residue: 0.3419 time to fit residues: 105.9058 Evaluate side-chains 206 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 2.127 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 244 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 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 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 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 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 447 SER Chi-restraints excluded: chain F residue 540 GLN 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 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 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 83 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 181 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN E 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.200234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.138296 restraints weight = 22596.180| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.54 r_work: 0.2958 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20592 Z= 0.165 Angle : 0.609 12.461 28131 Z= 0.299 Chirality : 0.045 0.265 3342 Planarity : 0.004 0.041 3438 Dihedral : 5.024 50.340 4263 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.93 % Allowed : 16.76 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2370 helix: 1.79 (0.29), residues: 402 sheet: 0.36 (0.17), residues: 867 loop : -0.68 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 47 HIS 0.004 0.001 HIS C 216 PHE 0.023 0.002 PHE A 383 TYR 0.008 0.001 TYR A 486 ARG 0.004 0.000 ARG E 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 45) link_NAG-ASN : angle 2.39483 ( 135) link_BETA1-4 : bond 0.00554 ( 30) link_BETA1-4 : angle 1.25027 ( 90) link_ALPHA1-2 : bond 0.00293 ( 3) link_ALPHA1-2 : angle 1.64718 ( 9) link_ALPHA1-3 : bond 0.01015 ( 3) link_ALPHA1-3 : angle 1.19408 ( 9) hydrogen bonds : bond 0.04977 ( 761) hydrogen bonds : angle 4.45757 ( 2067) SS BOND : bond 0.00443 ( 42) SS BOND : angle 1.81476 ( 84) covalent geometry : bond 0.00406 (20469) covalent geometry : angle 0.57566 (27804) *********************** 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 229 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7758 (t0) cc_final: 0.7441 (t0) REVERT: B 588 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7411 (mmm160) REVERT: B 655 LYS cc_start: 0.7764 (tptt) cc_final: 0.6635 (mtmt) REVERT: C 97 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8188 (mttp) REVERT: D 542 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7102 (mtp85) REVERT: D 588 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.7274 (mmm160) REVERT: E 500 ARG cc_start: 0.7481 (mtt90) cc_final: 0.7228 (mtt-85) REVERT: G 48 MET cc_start: 0.7413 (ptp) cc_final: 0.6724 (pmm) REVERT: G 80 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.3695 (mm) REVERT: I 35 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.5329 (t0) REVERT: K 48 MET cc_start: 0.7476 (ptp) cc_final: 0.7273 (ptp) REVERT: K 80 LEU cc_start: 0.4940 (OUTLIER) cc_final: 0.3728 (mm) REVERT: L 31 THR cc_start: 0.5430 (OUTLIER) cc_final: 0.5217 (p) outliers start: 62 outliers final: 41 residues processed: 219 average time/residue: 0.3282 time to fit residues: 109.6852 Evaluate side-chains 210 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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 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 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 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 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 529 THR 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 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 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 Chi-restraints excluded: chain L residue 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 0.6980 chunk 175 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 209 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 196 optimal weight: 30.0000 chunk 169 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN E 136 ASN K 81 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.200143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138107 restraints weight = 22723.533| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.44 r_work: 0.3045 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20592 Z= 0.167 Angle : 0.604 12.505 28131 Z= 0.298 Chirality : 0.045 0.267 3342 Planarity : 0.004 0.066 3438 Dihedral : 5.027 53.546 4263 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.93 % Allowed : 17.00 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2370 helix: 1.72 (0.29), residues: 402 sheet: 0.36 (0.17), residues: 867 loop : -0.72 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS I 77 PHE 0.022 0.002 PHE E 383 TYR 0.008 0.001 TYR E 384 ARG 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 45) link_NAG-ASN : angle 2.42025 ( 135) link_BETA1-4 : bond 0.00551 ( 30) link_BETA1-4 : angle 1.25509 ( 90) link_ALPHA1-2 : bond 0.00269 ( 3) link_ALPHA1-2 : angle 1.67741 ( 9) link_ALPHA1-3 : bond 0.00994 ( 3) link_ALPHA1-3 : angle 1.13455 ( 9) hydrogen bonds : bond 0.04943 ( 761) hydrogen bonds : angle 4.45113 ( 2067) SS BOND : bond 0.00446 ( 42) SS BOND : angle 1.79106 ( 84) covalent geometry : bond 0.00411 (20469) covalent geometry : angle 0.56923 (27804) *********************** 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 230 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 168 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7705 (t0) cc_final: 0.7382 (t0) REVERT: B 588 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.7444 (mmm160) REVERT: B 655 LYS cc_start: 0.7879 (tptt) cc_final: 0.6780 (mtmt) REVERT: C 129 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8776 (mt) REVERT: D 542 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7170 (mtp85) REVERT: D 588 ARG cc_start: 0.8337 (ttp-170) cc_final: 0.7294 (mmm160) REVERT: E 232 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7773 (mmtm) REVERT: E 500 ARG cc_start: 0.7444 (mtt90) cc_final: 0.7234 (mtt-85) REVERT: G 80 LEU cc_start: 0.5023 (OUTLIER) cc_final: 0.3762 (mm) REVERT: I 35 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5343 (t0) REVERT: K 48 MET cc_start: 0.7474 (ptp) cc_final: 0.7258 (ptp) REVERT: K 80 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.3824 (mm) REVERT: L 31 THR cc_start: 0.5396 (OUTLIER) cc_final: 0.5189 (p) outliers start: 62 outliers final: 46 residues processed: 219 average time/residue: 0.3310 time to fit residues: 109.8818 Evaluate side-chains 217 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP 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 244 THR 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 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 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 245 VAL Chi-restraints excluded: chain C residue 277 ILE 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 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 51 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 101 optimal weight: 0.9980 chunk 144 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 229 optimal weight: 40.0000 chunk 183 optimal weight: 30.0000 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.201994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141872 restraints weight = 22602.080| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.39 r_work: 0.2950 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20592 Z= 0.115 Angle : 0.552 11.491 28131 Z= 0.274 Chirality : 0.043 0.261 3342 Planarity : 0.003 0.059 3438 Dihedral : 4.759 54.696 4263 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.46 % Allowed : 17.56 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2370 helix: 1.94 (0.29), residues: 402 sheet: 0.39 (0.17), residues: 873 loop : -0.70 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS I 77 PHE 0.016 0.001 PHE E 383 TYR 0.009 0.001 TYR A 173 ARG 0.006 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 45) link_NAG-ASN : angle 2.31006 ( 135) link_BETA1-4 : bond 0.00522 ( 30) link_BETA1-4 : angle 1.17427 ( 90) link_ALPHA1-2 : bond 0.00275 ( 3) link_ALPHA1-2 : angle 1.69162 ( 9) link_ALPHA1-3 : bond 0.00987 ( 3) link_ALPHA1-3 : angle 1.06055 ( 9) hydrogen bonds : bond 0.04207 ( 761) hydrogen bonds : angle 4.31890 ( 2067) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.57853 ( 84) covalent geometry : bond 0.00266 (20469) covalent geometry : angle 0.51874 (27804) *********************** 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 216 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7678 (t0) cc_final: 0.7278 (t0) REVERT: B 588 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7316 (mmm160) REVERT: B 655 LYS cc_start: 0.7681 (tptt) cc_final: 0.6560 (mtmt) REVERT: D 540 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7729 (mp-120) REVERT: D 542 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7135 (mtp85) REVERT: D 588 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7254 (mmm160) REVERT: E 46 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7763 (ttpp) REVERT: E 232 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7699 (mmtm) REVERT: G 48 MET cc_start: 0.7288 (ptp) cc_final: 0.6710 (pmm) REVERT: G 80 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.3696 (mm) REVERT: I 35 ASN cc_start: 0.5829 (OUTLIER) cc_final: 0.5349 (t0) REVERT: K 48 MET cc_start: 0.7440 (ptp) cc_final: 0.7155 (ptp) REVERT: K 80 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.3809 (mm) REVERT: L 31 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.5285 (p) outliers start: 52 outliers final: 42 residues processed: 209 average time/residue: 0.3421 time to fit residues: 108.1377 Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 244 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 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 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 194 ILE 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 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 529 THR 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 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 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 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 62 optimal weight: 0.9980 chunk 144 optimal weight: 0.0670 chunk 165 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 236 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 193 optimal weight: 30.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.200479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143728 restraints weight = 22707.488| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.25 r_work: 0.2971 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20592 Z= 0.156 Angle : 0.596 12.177 28131 Z= 0.295 Chirality : 0.044 0.264 3342 Planarity : 0.004 0.072 3438 Dihedral : 4.811 55.347 4263 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.46 % Allowed : 17.52 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2370 helix: 1.88 (0.29), residues: 399 sheet: 0.40 (0.17), residues: 873 loop : -0.69 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 47 HIS 0.003 0.001 HIS C 216 PHE 0.022 0.002 PHE E 383 TYR 0.008 0.001 TYR E 384 ARG 0.012 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 45) link_NAG-ASN : angle 2.35838 ( 135) link_BETA1-4 : bond 0.00537 ( 30) link_BETA1-4 : angle 1.22855 ( 90) link_ALPHA1-2 : bond 0.00281 ( 3) link_ALPHA1-2 : angle 1.65391 ( 9) link_ALPHA1-3 : bond 0.00918 ( 3) link_ALPHA1-3 : angle 1.08474 ( 9) hydrogen bonds : bond 0.04777 ( 761) hydrogen bonds : angle 4.39743 ( 2067) SS BOND : bond 0.00442 ( 42) SS BOND : angle 1.85689 ( 84) covalent geometry : bond 0.00382 (20469) covalent geometry : angle 0.56200 (27804) ********************** 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 212 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7681 (t0) cc_final: 0.7348 (t0) REVERT: B 588 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7312 (mmm160) REVERT: B 655 LYS cc_start: 0.7713 (tptt) cc_final: 0.6582 (mtmt) REVERT: C 457 ASP cc_start: 0.7760 (t0) cc_final: 0.7527 (t0) REVERT: D 542 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7068 (mtp85) REVERT: D 588 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7173 (mmm160) REVERT: E 46 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7780 (ttpp) REVERT: G 48 MET cc_start: 0.7395 (ptp) cc_final: 0.6750 (pmm) REVERT: G 80 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.3638 (mm) REVERT: I 35 ASN cc_start: 0.5841 (OUTLIER) cc_final: 0.5345 (t0) REVERT: K 48 MET cc_start: 0.7442 (ptp) cc_final: 0.7144 (ptp) REVERT: K 80 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.3863 (mm) REVERT: L 31 THR cc_start: 0.5468 (OUTLIER) cc_final: 0.5258 (p) outliers start: 52 outliers final: 44 residues processed: 205 average time/residue: 0.3106 time to fit residues: 97.6961 Evaluate side-chains 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 244 THR 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 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 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 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 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 92 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.202550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142808 restraints weight = 22749.064| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.43 r_work: 0.3083 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20592 Z= 0.105 Angle : 0.539 11.161 28131 Z= 0.269 Chirality : 0.042 0.260 3342 Planarity : 0.004 0.066 3438 Dihedral : 4.603 56.398 4263 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.31 % Allowed : 17.61 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2370 helix: 2.06 (0.29), residues: 399 sheet: 0.52 (0.17), residues: 864 loop : -0.70 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.003 0.001 HIS I 77 PHE 0.015 0.001 PHE I 78 TYR 0.009 0.001 TYR A 173 ARG 0.010 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 45) link_NAG-ASN : angle 2.27813 ( 135) link_BETA1-4 : bond 0.00512 ( 30) link_BETA1-4 : angle 1.15050 ( 90) link_ALPHA1-2 : bond 0.00307 ( 3) link_ALPHA1-2 : angle 1.67507 ( 9) link_ALPHA1-3 : bond 0.00925 ( 3) link_ALPHA1-3 : angle 1.02737 ( 9) hydrogen bonds : bond 0.04002 ( 761) hydrogen bonds : angle 4.27076 ( 2067) SS BOND : bond 0.00371 ( 42) SS BOND : angle 1.64827 ( 84) covalent geometry : bond 0.00235 (20469) covalent geometry : angle 0.50489 (27804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12889.33 seconds wall clock time: 223 minutes 22.89 seconds (13402.89 seconds total)