Starting phenix.real_space_refine on Tue Jun 17 14:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl4_41361/06_2025/8tl4_41361.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl4_41361/06_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_41361/06_2025/8tl4_41361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl4_41361/06_2025/8tl4_41361.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl4_41361/06_2025/8tl4_41361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl4_41361/06_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-5710/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: 14.87, per 1000 atoms: 0.74 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: 5.66 Conformation dependent library (CDL) restraints added in 2.4 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: 2.65 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: 7.47 Time building geometry restraints manager: 6.66 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: 7.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 50.140 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.100 ------------------------------------------------------------------------------- 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 : 2.045 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: 0.3864 time to fit residues: 94.6645 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 : 2.359 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.202866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153147 restraints weight = 22682.981| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.16 r_work: 0.2930 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 9.435 28131 Z= 0.282 Chirality : 0.043 0.259 3342 Planarity : 0.004 0.063 3438 Dihedral : 8.731 77.577 4266 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.70 % Allowed : 15.16 % 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 2.09540 ( 135) link_BETA1-4 : bond 0.00696 ( 30) link_BETA1-4 : angle 1.03991 ( 90) link_ALPHA1-2 : bond 0.00694 ( 3) link_ALPHA1-2 : angle 1.61579 ( 9) link_ALPHA1-3 : bond 0.01292 ( 3) link_ALPHA1-3 : angle 1.71430 ( 9) hydrogen bonds : bond 0.04427 ( 761) hydrogen bonds : angle 4.55542 ( 2067) SS BOND : bond 0.00368 ( 42) SS BOND : angle 1.26531 ( 84) covalent geometry : bond 0.00315 (20469) covalent geometry : angle 0.54181 (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 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7709 (t0) cc_final: 0.7315 (t0) REVERT: B 515 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.5121 (pt) REVERT: B 588 ARG cc_start: 0.8354 (ttp-170) cc_final: 0.7424 (mmm160) REVERT: B 655 LYS cc_start: 0.7882 (tptt) cc_final: 0.6963 (ttmt) REVERT: C 457 ASP cc_start: 0.7602 (t0) cc_final: 0.7348 (t0) REVERT: D 542 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7290 (mtp85) REVERT: D 588 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7364 (mmm160) REVERT: K 35 ASN cc_start: 0.5216 (OUTLIER) cc_final: 0.4995 (t0) REVERT: K 48 MET cc_start: 0.7435 (ptp) cc_final: 0.6751 (pmm) outliers start: 36 outliers final: 14 residues processed: 196 average time/residue: 0.3610 time to fit residues: 105.8055 Evaluate side-chains 177 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain K residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 229 optimal weight: 40.0000 chunk 92 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 151 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.203279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150677 restraints weight = 22758.666| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 4.40 r_work: 0.2870 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20592 Z= 0.105 Angle : 0.519 9.410 28131 Z= 0.259 Chirality : 0.042 0.257 3342 Planarity : 0.003 0.052 3438 Dihedral : 7.060 57.264 4265 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.79 % Allowed : 15.82 % Favored : 82.39 % 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: 0.31 (0.18), residues: 2370 helix: 2.45 (0.29), residues: 384 sheet: 0.25 (0.17), residues: 855 loop : -0.57 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 479 HIS 0.003 0.001 HIS I 77 PHE 0.016 0.001 PHE G 78 TYR 0.008 0.001 TYR I 91 ARG 0.004 0.000 ARG E 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.15898 ( 135) link_BETA1-4 : bond 0.00557 ( 30) link_BETA1-4 : angle 1.07708 ( 90) link_ALPHA1-2 : bond 0.00541 ( 3) link_ALPHA1-2 : angle 1.50845 ( 9) link_ALPHA1-3 : bond 0.01245 ( 3) link_ALPHA1-3 : angle 1.32712 ( 9) hydrogen bonds : bond 0.03915 ( 761) hydrogen bonds : angle 4.37622 ( 2067) SS BOND : bond 0.00348 ( 42) SS BOND : angle 1.32373 ( 84) covalent geometry : bond 0.00235 (20469) covalent geometry : angle 0.48952 (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: 38 poor density : 166 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7772 (t0) cc_final: 0.7384 (t0) REVERT: B 542 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7029 (mtm-85) REVERT: B 588 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7245 (mmm160) REVERT: B 655 LYS cc_start: 0.7672 (tptt) cc_final: 0.6591 (mtmt) REVERT: C 457 ASP cc_start: 0.7638 (t0) cc_final: 0.7352 (t0) REVERT: D 540 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7757 (mp-120) REVERT: D 542 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7168 (mtp85) REVERT: D 584 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8246 (mt-10) REVERT: D 588 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7178 (mmm160) REVERT: F 536 THR cc_start: 0.8520 (p) cc_final: 0.7671 (p) REVERT: F 540 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7758 (mp-120) REVERT: K 48 MET cc_start: 0.7466 (ptp) cc_final: 0.6791 (pmm) outliers start: 38 outliers final: 17 residues processed: 193 average time/residue: 0.4599 time to fit residues: 135.2024 Evaluate side-chains 178 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 3.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 277 ILE 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 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 D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 134 VAL 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: 40.0000 chunk 215 optimal weight: 20.0000 chunk 200 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN F 607 ASN I 81 HIS K 35AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.196615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138316 restraints weight = 22662.415| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.23 r_work: 0.2988 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20592 Z= 0.257 Angle : 0.706 13.145 28131 Z= 0.345 Chirality : 0.049 0.263 3342 Planarity : 0.004 0.050 3438 Dihedral : 6.528 48.375 4263 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.83 % Allowed : 16.24 % Favored : 80.93 % 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: 0.01 (0.17), residues: 2370 helix: 1.73 (0.29), residues: 387 sheet: 0.19 (0.17), residues: 873 loop : -0.71 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.005 0.001 HIS C 374 PHE 0.028 0.002 PHE E 383 TYR 0.013 0.002 TYR A 486 ARG 0.003 0.000 ARG F 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 45) link_NAG-ASN : angle 2.55511 ( 135) link_BETA1-4 : bond 0.00632 ( 30) link_BETA1-4 : angle 1.41112 ( 90) link_ALPHA1-2 : bond 0.00380 ( 3) link_ALPHA1-2 : angle 1.51440 ( 9) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.31100 ( 9) hydrogen bonds : bond 0.06294 ( 761) hydrogen bonds : angle 4.73790 ( 2067) SS BOND : bond 0.00514 ( 42) SS BOND : angle 2.02025 ( 84) covalent geometry : bond 0.00645 (20469) covalent geometry : angle 0.67298 (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 227 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 2.390 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: 0.9149 (p) cc_final: 0.8890 (t) REVERT: A 457 ASP cc_start: 0.7804 (t0) cc_final: 0.7454 (t0) REVERT: B 588 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.7413 (mmm160) REVERT: B 655 LYS cc_start: 0.7833 (tptt) cc_final: 0.6754 (mtmt) REVERT: D 542 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7239 (mtp85) REVERT: D 588 ARG cc_start: 0.8400 (ttp-170) cc_final: 0.7343 (mmm160) REVERT: G 48 MET cc_start: 0.7196 (ptp) cc_final: 0.6608 (pmm) REVERT: G 80 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.3615 (mm) REVERT: I 35 ASN cc_start: 0.5776 (OUTLIER) cc_final: 0.5288 (t0) REVERT: I 80 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.3959 (mm) REVERT: K 80 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.3676 (mm) outliers start: 60 outliers final: 30 residues processed: 215 average time/residue: 0.3407 time to fit residues: 113.1136 Evaluate side-chains 195 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 2.140 ------------------------------------------------------------------------------- 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 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 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 80 LEU 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: 0.9980 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 F 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.200303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138170 restraints weight = 22721.162| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.46 r_work: 0.2924 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20592 Z= 0.123 Angle : 0.573 10.224 28131 Z= 0.283 Chirality : 0.043 0.259 3342 Planarity : 0.003 0.043 3438 Dihedral : 5.770 50.928 4263 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.79 % Allowed : 16.90 % 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: 0.07 (0.17), residues: 2370 helix: 1.51 (0.28), residues: 420 sheet: 0.35 (0.17), residues: 846 loop : -0.73 (0.18), residues: 1104 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 0.018 0.001 PHE A 383 TYR 0.008 0.001 TYR A 173 ARG 0.004 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00234 ( 45) link_NAG-ASN : angle 2.40686 ( 135) link_BETA1-4 : bond 0.00564 ( 30) link_BETA1-4 : angle 1.22102 ( 90) link_ALPHA1-2 : bond 0.00338 ( 3) link_ALPHA1-2 : angle 1.63851 ( 9) link_ALPHA1-3 : bond 0.01175 ( 3) link_ALPHA1-3 : angle 1.32850 ( 9) hydrogen bonds : bond 0.04642 ( 761) hydrogen bonds : angle 4.49244 ( 2067) SS BOND : bond 0.00374 ( 42) SS BOND : angle 1.64574 ( 84) covalent geometry : bond 0.00285 (20469) covalent geometry : angle 0.53801 (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 222 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 2.999 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: 0.9081 (p) cc_final: 0.8878 (t) REVERT: A 72 HIS cc_start: 0.5887 (OUTLIER) cc_final: 0.5630 (t-90) REVERT: A 457 ASP cc_start: 0.7796 (t0) cc_final: 0.7425 (t0) REVERT: B 588 ARG cc_start: 0.8311 (ttp-170) cc_final: 0.7267 (mmm160) REVERT: B 655 LYS cc_start: 0.7678 (tptt) cc_final: 0.6576 (mtmt) REVERT: C 457 ASP cc_start: 0.7808 (t0) cc_final: 0.7582 (t0) REVERT: D 540 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7602 (mp-120) REVERT: D 542 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7121 (mtp85) REVERT: D 588 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7225 (mmm160) REVERT: G 48 MET cc_start: 0.7331 (ptp) cc_final: 0.6700 (pmm) REVERT: G 80 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.3614 (mm) REVERT: I 35 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.5304 (t0) REVERT: I 80 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.3981 (mm) REVERT: K 80 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.3623 (mm) outliers start: 59 outliers final: 31 residues processed: 208 average time/residue: 0.4173 time to fit residues: 131.3053 Evaluate side-chains 197 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 499 THR 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 184 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 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 I residue 80 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: 0.6980 chunk 114 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.200381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141913 restraints weight = 22668.041| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.26 r_work: 0.2973 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1589 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= 0.121 Angle : 0.556 11.052 28131 Z= 0.275 Chirality : 0.043 0.261 3342 Planarity : 0.003 0.042 3438 Dihedral : 5.146 49.233 4263 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 17.09 % 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: 0.24 (0.18), residues: 2370 helix: 1.93 (0.29), residues: 402 sheet: 0.38 (0.17), residues: 867 loop : -0.65 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 47 HIS 0.003 0.001 HIS I 77 PHE 0.017 0.001 PHE A 383 TYR 0.007 0.001 TYR A 173 ARG 0.004 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 45) link_NAG-ASN : angle 2.28622 ( 135) link_BETA1-4 : bond 0.00545 ( 30) link_BETA1-4 : angle 1.18568 ( 90) link_ALPHA1-2 : bond 0.00348 ( 3) link_ALPHA1-2 : angle 1.62475 ( 9) link_ALPHA1-3 : bond 0.01137 ( 3) link_ALPHA1-3 : angle 1.32073 ( 9) hydrogen bonds : bond 0.04316 ( 761) hydrogen bonds : angle 4.40027 ( 2067) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.60369 ( 84) covalent geometry : bond 0.00283 (20469) covalent geometry : angle 0.52336 (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: 55 poor density : 164 time to evaluate : 2.122 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: 0.9079 (p) cc_final: 0.8876 (t) REVERT: A 72 HIS cc_start: 0.5887 (OUTLIER) cc_final: 0.5631 (t-90) REVERT: A 457 ASP cc_start: 0.7756 (t0) cc_final: 0.7381 (t0) REVERT: B 588 ARG cc_start: 0.8306 (ttp-170) cc_final: 0.7309 (mmm160) REVERT: B 655 LYS cc_start: 0.7673 (tptt) cc_final: 0.6565 (mtmt) REVERT: C 457 ASP cc_start: 0.7788 (t0) cc_final: 0.7517 (t0) REVERT: D 542 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7100 (mtp85) REVERT: D 588 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7241 (mmm160) REVERT: E 232 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7940 (mmtm) REVERT: G 48 MET cc_start: 0.7452 (ptp) cc_final: 0.6749 (pmm) REVERT: G 80 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.3592 (mm) REVERT: I 35 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.5305 (t0) REVERT: I 80 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.3937 (mm) REVERT: K 80 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.3672 (mm) REVERT: L 31 THR cc_start: 0.5590 (OUTLIER) cc_final: 0.5343 (p) outliers start: 55 outliers final: 37 residues processed: 205 average time/residue: 0.4010 time to fit residues: 125.1308 Evaluate side-chains 205 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 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 447 SER Chi-restraints excluded: chain A residue 499 THR 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 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 202 THR 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 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 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 I residue 80 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: 5.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 187 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 chunk 181 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.201951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139786 restraints weight = 22643.624| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.43 r_work: 0.2949 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.003 0.059 20592 Z= 0.124 Angle : 0.555 11.597 28131 Z= 0.274 Chirality : 0.043 0.262 3342 Planarity : 0.003 0.040 3438 Dihedral : 4.898 47.437 4263 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.69 % Allowed : 17.19 % Favored : 80.12 % 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: 0.26 (0.18), residues: 2370 helix: 1.95 (0.29), residues: 402 sheet: 0.40 (0.17), residues: 867 loop : -0.65 (0.19), residues: 1101 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 A 383 TYR 0.007 0.001 TYR A 173 ARG 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 45) link_NAG-ASN : angle 2.27978 ( 135) link_BETA1-4 : bond 0.00538 ( 30) link_BETA1-4 : angle 1.17188 ( 90) link_ALPHA1-2 : bond 0.00329 ( 3) link_ALPHA1-2 : angle 1.64150 ( 9) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 1.21481 ( 9) hydrogen bonds : bond 0.04316 ( 761) hydrogen bonds : angle 4.36777 ( 2067) SS BOND : bond 0.00411 ( 42) SS BOND : angle 1.62856 ( 84) covalent geometry : bond 0.00293 (20469) covalent geometry : angle 0.52216 (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 221 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 164 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9075 (p) cc_final: 0.8852 (t) REVERT: A 72 HIS cc_start: 0.5873 (OUTLIER) cc_final: 0.5621 (t-90) REVERT: A 457 ASP cc_start: 0.7695 (t0) cc_final: 0.7308 (t0) REVERT: B 588 ARG cc_start: 0.8324 (ttp-170) cc_final: 0.7348 (mmm160) REVERT: B 655 LYS cc_start: 0.7690 (tptt) cc_final: 0.6580 (mtmt) REVERT: C 97 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8112 (mttp) REVERT: C 457 ASP cc_start: 0.7811 (t0) cc_final: 0.7509 (t0) REVERT: D 540 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7734 (mp-120) REVERT: D 542 ARG cc_start: 0.7647 (mtm-85) cc_final: 0.7115 (mtp85) REVERT: D 588 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.7264 (mmm160) REVERT: E 232 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8056 (mmtm) REVERT: G 48 MET cc_start: 0.7390 (ptp) cc_final: 0.6691 (pmm) REVERT: G 80 LEU cc_start: 0.4842 (OUTLIER) cc_final: 0.3605 (mm) REVERT: I 35 ASN cc_start: 0.5768 (OUTLIER) cc_final: 0.5316 (t0) REVERT: I 80 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.3875 (mm) REVERT: K 80 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.3718 (mm) REVERT: L 31 THR cc_start: 0.5540 (OUTLIER) cc_final: 0.5283 (p) outliers start: 57 outliers final: 43 residues processed: 208 average time/residue: 0.4609 time to fit residues: 146.5017 Evaluate side-chains 212 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 499 THR 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 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 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 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 I residue 80 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: 3.9990 chunk 67 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 0.0980 chunk 209 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 196 optimal weight: 30.0000 chunk 169 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.201239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139456 restraints weight = 22750.542| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.46 r_work: 0.3059 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20592 Z= 0.143 Angle : 0.578 11.807 28131 Z= 0.285 Chirality : 0.044 0.265 3342 Planarity : 0.004 0.066 3438 Dihedral : 4.828 46.014 4263 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.97 % Allowed : 16.86 % 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: 0.23 (0.18), residues: 2370 helix: 1.88 (0.29), residues: 402 sheet: 0.39 (0.17), residues: 867 loop : -0.66 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 47 HIS 0.003 0.001 HIS C 216 PHE 0.020 0.002 PHE A 383 TYR 0.007 0.001 TYR A 486 ARG 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00217 ( 45) link_NAG-ASN : angle 2.30868 ( 135) link_BETA1-4 : bond 0.00540 ( 30) link_BETA1-4 : angle 1.19543 ( 90) link_ALPHA1-2 : bond 0.00307 ( 3) link_ALPHA1-2 : angle 1.63451 ( 9) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.15427 ( 9) hydrogen bonds : bond 0.04610 ( 761) hydrogen bonds : angle 4.39888 ( 2067) SS BOND : bond 0.00420 ( 42) SS BOND : angle 1.66911 ( 84) covalent geometry : bond 0.00345 (20469) covalent geometry : angle 0.54548 (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 226 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 5.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9104 (p) cc_final: 0.8886 (t) REVERT: A 72 HIS cc_start: 0.5961 (OUTLIER) cc_final: 0.5619 (t-90) REVERT: A 457 ASP cc_start: 0.7631 (t0) cc_final: 0.7257 (t0) REVERT: B 542 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7259 (mtm-85) REVERT: B 588 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7416 (mmm160) REVERT: B 655 LYS cc_start: 0.7776 (tptt) cc_final: 0.6670 (mtmt) REVERT: C 348 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7000 (mp-120) REVERT: D 542 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7141 (mtp85) REVERT: D 588 ARG cc_start: 0.8343 (ttp-170) cc_final: 0.7313 (mmm160) REVERT: E 232 LYS cc_start: 0.8253 (mmmm) cc_final: 0.8052 (mmtm) REVERT: G 48 MET cc_start: 0.7423 (ptp) cc_final: 0.6737 (pmm) REVERT: G 80 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.3611 (mm) REVERT: I 35 ASN cc_start: 0.5837 (OUTLIER) cc_final: 0.5336 (t0) REVERT: I 80 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.3860 (mm) REVERT: K 48 MET cc_start: 0.7217 (ptp) cc_final: 0.6684 (pmm) REVERT: K 80 LEU cc_start: 0.4987 (OUTLIER) cc_final: 0.3851 (mm) REVERT: L 31 THR cc_start: 0.5488 (OUTLIER) cc_final: 0.5278 (p) outliers start: 63 outliers final: 45 residues processed: 215 average time/residue: 0.5645 time to fit residues: 184.6278 Evaluate side-chains 214 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 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 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 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 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 80 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: 0.7980 chunk 219 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 144 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 chunk 229 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.202645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140312 restraints weight = 22595.851| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.2972 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 20592 Z= 0.104 Angle : 0.540 11.179 28131 Z= 0.269 Chirality : 0.042 0.261 3342 Planarity : 0.003 0.060 3438 Dihedral : 4.661 44.796 4263 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: 0.30 (0.18), residues: 2370 helix: 2.05 (0.29), residues: 402 sheet: 0.41 (0.17), residues: 873 loop : -0.65 (0.19), residues: 1095 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 0.015 0.001 PHE E 383 TYR 0.009 0.001 TYR A 173 ARG 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 45) link_NAG-ASN : angle 2.26744 ( 135) link_BETA1-4 : bond 0.00518 ( 30) link_BETA1-4 : angle 1.15061 ( 90) link_ALPHA1-2 : bond 0.00307 ( 3) link_ALPHA1-2 : angle 1.66598 ( 9) link_ALPHA1-3 : bond 0.01029 ( 3) link_ALPHA1-3 : angle 1.11263 ( 9) hydrogen bonds : bond 0.04086 ( 761) hydrogen bonds : angle 4.32140 ( 2067) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.59792 ( 84) covalent geometry : bond 0.00233 (20469) covalent geometry : angle 0.50659 (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 209 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9057 (p) cc_final: 0.8851 (t) REVERT: A 72 HIS cc_start: 0.5859 (OUTLIER) cc_final: 0.5566 (t-90) REVERT: A 457 ASP cc_start: 0.7664 (t0) cc_final: 0.7274 (t0) REVERT: B 542 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7182 (mtm-85) REVERT: B 588 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.7281 (mmm160) REVERT: B 655 LYS cc_start: 0.7638 (tptt) cc_final: 0.6532 (mtmt) REVERT: C 348 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6756 (mp-120) REVERT: C 488 VAL cc_start: 0.8729 (OUTLIER) cc_final: 0.8468 (t) REVERT: D 540 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7690 (mp-120) REVERT: D 542 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7090 (mtp85) REVERT: D 588 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7200 (mmm160) REVERT: E 46 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7738 (ttpp) REVERT: E 232 LYS cc_start: 0.8254 (mmmm) cc_final: 0.8047 (mmtm) REVERT: F 536 THR cc_start: 0.8390 (p) cc_final: 0.7561 (p) REVERT: F 540 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7763 (mp-120) REVERT: G 48 MET cc_start: 0.7422 (ptp) cc_final: 0.6749 (pmm) REVERT: G 80 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.3621 (mm) REVERT: I 35 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5303 (t0) REVERT: I 80 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.3924 (mm) REVERT: K 48 MET cc_start: 0.7226 (ptp) cc_final: 0.6637 (pmm) REVERT: K 80 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.3902 (mm) REVERT: L 31 THR cc_start: 0.5490 (OUTLIER) cc_final: 0.5272 (p) outliers start: 49 outliers final: 36 residues processed: 202 average time/residue: 0.7730 time to fit residues: 241.6075 Evaluate side-chains 204 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG 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 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 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 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 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 G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 80 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: 0.0770 chunk 165 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 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: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 GLN 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 = 0.202031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140800 restraints weight = 22777.513| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.47 r_work: 0.3069 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20592 Z= 0.124 Angle : 0.553 11.376 28131 Z= 0.275 Chirality : 0.043 0.263 3342 Planarity : 0.003 0.056 3438 Dihedral : 4.602 42.785 4263 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 17.75 % 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: 0.32 (0.18), residues: 2370 helix: 2.03 (0.29), residues: 402 sheet: 0.44 (0.17), residues: 867 loop : -0.63 (0.19), residues: 1101 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 0.017 0.001 PHE E 383 TYR 0.007 0.001 TYR A 173 ARG 0.005 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 45) link_NAG-ASN : angle 2.25024 ( 135) link_BETA1-4 : bond 0.00525 ( 30) link_BETA1-4 : angle 1.15108 ( 90) link_ALPHA1-2 : bond 0.00319 ( 3) link_ALPHA1-2 : angle 1.63546 ( 9) link_ALPHA1-3 : bond 0.00972 ( 3) link_ALPHA1-3 : angle 1.08425 ( 9) hydrogen bonds : bond 0.04250 ( 761) hydrogen bonds : angle 4.32609 ( 2067) SS BOND : bond 0.00394 ( 42) SS BOND : angle 1.68496 ( 84) covalent geometry : bond 0.00293 (20469) covalent geometry : angle 0.52067 (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 208 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.9117 (p) cc_final: 0.8891 (t) REVERT: A 72 HIS cc_start: 0.5962 (OUTLIER) cc_final: 0.5616 (t-90) REVERT: A 457 ASP cc_start: 0.7610 (t0) cc_final: 0.7227 (t0) REVERT: B 542 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7240 (mtm-85) REVERT: B 588 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.7439 (mmm160) REVERT: B 655 LYS cc_start: 0.7799 (tptt) cc_final: 0.6701 (mtmt) REVERT: C 348 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6988 (mp-120) REVERT: C 457 ASP cc_start: 0.7689 (t0) cc_final: 0.7434 (t0) REVERT: D 540 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7820 (mp-120) REVERT: D 542 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7161 (mtp85) REVERT: D 588 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.7367 (mmm160) REVERT: E 46 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7864 (ttpp) REVERT: E 500 ARG cc_start: 0.7695 (mtt90) cc_final: 0.7467 (mtt-85) REVERT: G 80 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.3638 (mm) REVERT: I 35 ASN cc_start: 0.5824 (OUTLIER) cc_final: 0.5306 (t0) REVERT: I 80 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.3882 (mm) REVERT: K 48 MET cc_start: 0.7207 (ptp) cc_final: 0.6614 (pmm) REVERT: K 80 LEU cc_start: 0.4998 (OUTLIER) cc_final: 0.3890 (mm) REVERT: L 31 THR cc_start: 0.5505 (OUTLIER) cc_final: 0.5287 (p) outliers start: 48 outliers final: 37 residues processed: 201 average time/residue: 0.3506 time to fit residues: 106.2712 Evaluate side-chains 204 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 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 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 348 GLN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR 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 184 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 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 I residue 80 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: 0.8980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 0.0470 chunk 178 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 93 optimal weight: 0.7980 chunk 222 optimal weight: 8.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 348 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.202895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.141580 restraints weight = 22794.372| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.50 r_work: 0.3028 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20592 Z= 0.103 Angle : 0.534 11.008 28131 Z= 0.266 Chirality : 0.042 0.261 3342 Planarity : 0.003 0.071 3438 Dihedral : 4.470 40.199 4263 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 0.37 (0.18), residues: 2370 helix: 2.10 (0.29), residues: 402 sheet: 0.52 (0.17), residues: 861 loop : -0.64 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.005 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 45) link_NAG-ASN : angle 2.23082 ( 135) link_BETA1-4 : bond 0.00511 ( 30) link_BETA1-4 : angle 1.12354 ( 90) link_ALPHA1-2 : bond 0.00321 ( 3) link_ALPHA1-2 : angle 1.64430 ( 9) link_ALPHA1-3 : bond 0.00977 ( 3) link_ALPHA1-3 : angle 1.06786 ( 9) hydrogen bonds : bond 0.03968 ( 761) hydrogen bonds : angle 4.27674 ( 2067) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.53426 ( 84) covalent geometry : bond 0.00234 (20469) covalent geometry : angle 0.50149 (27804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14616.34 seconds wall clock time: 264 minutes 47.29 seconds (15887.29 seconds total)