Starting phenix.real_space_refine on Tue Nov 19 20:11:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_41361.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_41361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_41361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_41361.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl4_41361/11_2024/8tl4_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-5513/modules/chem_data/mon_lib" Total number of atoms: 20055 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 858 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.70, per 1000 atoms: 0.63 Number of scatterers: 20055 At special positions: 0 Unit cell: (154.602, 150.284, 145.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 4017 8.00 N 3366 7.00 C 12546 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19955 O5 NAG C 605 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Y 4 " - " MAN Y 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 88 " " NAG A 606 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN C 448 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 448 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 363 " Time building additional restraints: 4.78 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: 2.85 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: 7.50 Time building geometry restraints manager: 5.63 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 46.060 Find NCS groups from input model: 1.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.830 ------------------------------------------------------------------------------- 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 20469 Z= 0.272 Angle : 0.637 7.770 27804 Z= 0.310 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 *********************** 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 : 2.149 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: 0.3938 time to fit residues: 96.7794 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 : 2.364 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9402 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20469 Z= 0.220 Angle : 0.548 9.970 27804 Z= 0.279 Chirality : 0.044 0.262 3342 Planarity : 0.004 0.064 3438 Dihedral : 8.795 78.135 4266 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.75 % Allowed : 15.11 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2370 helix: 2.43 (0.30), residues: 384 sheet: 0.18 (0.17), residues: 822 loop : -0.58 (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 0.018 0.002 PHE A 383 TYR 0.013 0.001 TYR G 90 ARG 0.005 0.000 ARG E 151 *********************** 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 212 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7514 (t0) cc_final: 0.7309 (t0) REVERT: B 515 ILE cc_start: 0.5287 (OUTLIER) cc_final: 0.5073 (pt) REVERT: B 588 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7319 (mmm160) REVERT: B 655 LYS cc_start: 0.7922 (tptt) cc_final: 0.7017 (ttmt) REVERT: C 457 ASP cc_start: 0.7484 (t0) cc_final: 0.7229 (t0) REVERT: D 542 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7284 (mtp85) REVERT: D 588 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7240 (mmm160) REVERT: K 35 ASN cc_start: 0.5322 (OUTLIER) cc_final: 0.5049 (t0) REVERT: K 48 MET cc_start: 0.7305 (ptp) cc_final: 0.6710 (pmm) outliers start: 37 outliers final: 13 residues processed: 200 average time/residue: 0.3475 time to fit residues: 105.5419 Evaluate side-chains 180 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 235 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 C 216 HIS E 136 ASN F 607 ASN I 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 20469 Z= 0.604 Angle : 0.786 13.422 27804 Z= 0.391 Chirality : 0.053 0.269 3342 Planarity : 0.005 0.063 3438 Dihedral : 8.149 67.183 4265 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.35 % Allowed : 15.96 % Favored : 80.69 % 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 (0.17), residues: 2370 helix: 0.80 (0.28), residues: 423 sheet: 0.13 (0.17), residues: 822 loop : -0.89 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 427 HIS 0.005 0.002 HIS G 99 PHE 0.031 0.003 PHE E 383 TYR 0.016 0.002 TYR E 384 ARG 0.005 0.001 ARG E 327 *********************** 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 238 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 167 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 THR cc_start: 0.8609 (t) cc_final: 0.8404 (p) REVERT: A 457 ASP cc_start: 0.7691 (t0) cc_final: 0.7351 (t0) REVERT: B 542 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7310 (mtm-85) REVERT: B 588 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7423 (mmm160) REVERT: B 655 LYS cc_start: 0.8020 (tptt) cc_final: 0.6975 (mtmt) REVERT: C 290 THR cc_start: 0.8751 (t) cc_final: 0.8529 (p) REVERT: C 457 ASP cc_start: 0.7562 (t0) cc_final: 0.7216 (t0) REVERT: D 542 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7329 (mtp85) REVERT: E 321 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (m-30) REVERT: G 48 MET cc_start: 0.6970 (ptp) cc_final: 0.6640 (pmm) REVERT: G 80 LEU cc_start: 0.4966 (OUTLIER) cc_final: 0.3752 (mm) REVERT: I 48 MET cc_start: 0.7292 (ptp) cc_final: 0.6675 (pmm) REVERT: I 80 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.3961 (mm) REVERT: K 48 MET cc_start: 0.7413 (ptp) cc_final: 0.6724 (pmm) REVERT: K 80 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.3696 (mm) outliers start: 71 outliers final: 38 residues processed: 226 average time/residue: 0.3369 time to fit residues: 117.8793 Evaluate side-chains 199 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 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 605 CYS Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 50.0000 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 114 GLN C 136 ASN E 136 ASN F 652 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20469 Z= 0.203 Angle : 0.551 11.564 27804 Z= 0.281 Chirality : 0.044 0.258 3342 Planarity : 0.003 0.053 3438 Dihedral : 6.834 59.852 4265 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.79 % Allowed : 17.28 % Favored : 79.93 % 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: -0.14 (0.17), residues: 2370 helix: 1.33 (0.28), residues: 420 sheet: 0.21 (0.17), residues: 852 loop : -0.86 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 PHE 0.019 0.001 PHE C 383 TYR 0.010 0.001 TYR A 173 ARG 0.003 0.000 ARG C 444 *********************** 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 226 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7572 (t0) cc_final: 0.7214 (t0) REVERT: B 588 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7375 (mmm160) REVERT: B 655 LYS cc_start: 0.7996 (tptt) cc_final: 0.6957 (mtmt) REVERT: C 457 ASP cc_start: 0.7494 (t0) cc_final: 0.7180 (t0) REVERT: D 540 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7689 (mp-120) REVERT: D 542 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7367 (mtp85) REVERT: D 588 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7308 (mmm160) REVERT: F 536 THR cc_start: 0.8803 (p) cc_final: 0.7977 (p) REVERT: F 540 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7870 (mp-120) REVERT: G 48 MET cc_start: 0.7106 (ptp) cc_final: 0.6781 (pmm) REVERT: I 35 ASN cc_start: 0.5826 (OUTLIER) cc_final: 0.5372 (t0) REVERT: K 35 ASN cc_start: 0.5508 (OUTLIER) cc_final: 0.5104 (t0) REVERT: K 80 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.3816 (mm) outliers start: 59 outliers final: 30 residues processed: 214 average time/residue: 0.3392 time to fit residues: 111.0207 Evaluate side-chains 199 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 501 CYS 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 194 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 30.0000 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 58 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 K 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 20469 Z= 0.461 Angle : 0.698 10.640 27804 Z= 0.347 Chirality : 0.049 0.270 3342 Planarity : 0.005 0.079 3438 Dihedral : 6.660 59.671 4265 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.87 % Allowed : 17.14 % Favored : 78.99 % 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 (0.17), residues: 2370 helix: 1.00 (0.28), residues: 423 sheet: 0.18 (0.17), residues: 846 loop : -0.97 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 427 HIS 0.004 0.001 HIS K 99 PHE 0.029 0.002 PHE E 383 TYR 0.013 0.002 TYR E 384 ARG 0.004 0.000 ARG A 444 *********************** 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 249 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 167 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7629 (t0) cc_final: 0.7373 (t0) REVERT: B 588 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7448 (mmm160) REVERT: B 655 LYS cc_start: 0.8058 (tptt) cc_final: 0.7007 (mtmt) REVERT: C 430 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8313 (pt) REVERT: C 457 ASP cc_start: 0.7542 (t0) cc_final: 0.7161 (t0) REVERT: D 542 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7340 (mtp85) REVERT: D 588 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7338 (mmm160) REVERT: G 48 MET cc_start: 0.7125 (ptp) cc_final: 0.6692 (pmm) REVERT: G 80 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.3647 (mm) REVERT: I 35 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5369 (t0) REVERT: K 80 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.3898 (mm) outliers start: 82 outliers final: 50 residues processed: 234 average time/residue: 0.3273 time to fit residues: 120.4148 Evaluate side-chains 219 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER 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 605 CYS 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 68 VAL 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 244 THR Chi-restraints excluded: chain C residue 265 LEU 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 430 ILE Chi-restraints excluded: chain C residue 433 CYS 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 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 136 ASN E 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20469 Z= 0.249 Angle : 0.579 10.261 27804 Z= 0.293 Chirality : 0.045 0.262 3342 Planarity : 0.004 0.063 3438 Dihedral : 5.973 58.038 4265 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.35 % Allowed : 17.66 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2370 helix: 1.28 (0.28), residues: 420 sheet: 0.28 (0.17), residues: 846 loop : -0.96 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 PHE 0.022 0.002 PHE C 383 TYR 0.009 0.001 TYR A 173 ARG 0.004 0.000 ARG E 151 *********************** 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 240 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7558 (t0) cc_final: 0.7300 (t0) REVERT: B 588 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7388 (mmm160) REVERT: B 655 LYS cc_start: 0.8041 (tptt) cc_final: 0.6973 (mtmt) REVERT: C 457 ASP cc_start: 0.7516 (t0) cc_final: 0.7270 (t0) REVERT: D 540 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7679 (mp-120) REVERT: D 542 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7345 (mtp85) REVERT: D 588 ARG cc_start: 0.8024 (ttp-170) cc_final: 0.7249 (mmm160) REVERT: G 48 MET cc_start: 0.7182 (ptp) cc_final: 0.6668 (pmm) REVERT: G 80 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.3618 (mm) REVERT: I 35 ASN cc_start: 0.5907 (OUTLIER) cc_final: 0.5405 (t0) REVERT: K 48 MET cc_start: 0.7235 (ptp) cc_final: 0.6685 (pmm) REVERT: K 80 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.3921 (mm) outliers start: 71 outliers final: 47 residues processed: 228 average time/residue: 0.3471 time to fit residues: 121.4295 Evaluate side-chains 218 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 195 optimal weight: 30.0000 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 50.0000 chunk 144 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN E 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20469 Z= 0.307 Angle : 0.607 12.335 27804 Z= 0.306 Chirality : 0.046 0.266 3342 Planarity : 0.004 0.060 3438 Dihedral : 5.821 57.897 4265 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.59 % Allowed : 17.47 % Favored : 78.94 % 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: -0.15 (0.17), residues: 2370 helix: 1.28 (0.28), residues: 420 sheet: 0.31 (0.17), residues: 846 loop : -0.94 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 PHE 0.024 0.002 PHE C 383 TYR 0.009 0.001 TYR E 384 ARG 0.004 0.000 ARG C 444 *********************** 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 246 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 170 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7570 (t0) cc_final: 0.7305 (t0) REVERT: B 588 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7403 (mmm160) REVERT: B 655 LYS cc_start: 0.8055 (tptt) cc_final: 0.6977 (mtmt) REVERT: C 129 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.8940 (mt) REVERT: C 430 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8363 (pt) REVERT: C 457 ASP cc_start: 0.7535 (t0) cc_final: 0.7282 (t0) REVERT: C 478 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7691 (m110) REVERT: D 540 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7648 (mp-120) REVERT: D 542 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7369 (mtp85) REVERT: D 588 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7276 (mmm160) REVERT: G 48 MET cc_start: 0.7284 (ptp) cc_final: 0.6724 (pmm) REVERT: G 80 LEU cc_start: 0.4850 (OUTLIER) cc_final: 0.3641 (mm) REVERT: I 35 ASN cc_start: 0.5879 (OUTLIER) cc_final: 0.5353 (t0) REVERT: K 48 MET cc_start: 0.7284 (ptp) cc_final: 0.6665 (pmm) outliers start: 76 outliers final: 57 residues processed: 235 average time/residue: 0.3217 time to fit residues: 117.0287 Evaluate side-chains 231 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER 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 129 LEU Chi-restraints excluded: chain C residue 136 ASN 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 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 LEU 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 413 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL 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 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 35 ASN Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20469 Z= 0.202 Angle : 0.557 11.636 27804 Z= 0.283 Chirality : 0.044 0.262 3342 Planarity : 0.004 0.055 3438 Dihedral : 5.529 56.505 4265 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.21 % Allowed : 17.99 % Favored : 78.80 % 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: 0.00 (0.18), residues: 2370 helix: 1.72 (0.29), residues: 402 sheet: 0.26 (0.17), residues: 879 loop : -0.84 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS I 77 PHE 0.018 0.001 PHE E 383 TYR 0.010 0.001 TYR A 173 ARG 0.011 0.000 ARG A 500 *********************** 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 242 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 2.107 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: 0.9182 (p) cc_final: 0.8905 (t) REVERT: A 457 ASP cc_start: 0.7506 (t0) cc_final: 0.7238 (t0) REVERT: B 588 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7388 (mmm160) REVERT: B 655 LYS cc_start: 0.7993 (tptt) cc_final: 0.6886 (mtmt) REVERT: C 129 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.8909 (mt) REVERT: C 430 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8364 (pt) REVERT: C 457 ASP cc_start: 0.7525 (t0) cc_final: 0.7265 (t0) REVERT: D 540 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7698 (mp-120) REVERT: D 542 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7282 (mtp85) REVERT: D 588 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7293 (mmm160) REVERT: F 540 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7831 (mp-120) REVERT: G 48 MET cc_start: 0.7251 (ptp) cc_final: 0.6718 (pmm) REVERT: G 80 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.3633 (mm) REVERT: I 35 ASN cc_start: 0.5890 (OUTLIER) cc_final: 0.5373 (t0) outliers start: 68 outliers final: 50 residues processed: 231 average time/residue: 0.3361 time to fit residues: 118.9379 Evaluate side-chains 227 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 244 THR 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 129 LEU 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 225 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 LEU 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 430 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 467 THR 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 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 128 THR 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 202 THR 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 G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.0980 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 194 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20469 Z= 0.276 Angle : 0.589 12.156 27804 Z= 0.299 Chirality : 0.045 0.266 3342 Planarity : 0.004 0.054 3438 Dihedral : 5.441 56.033 4263 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.68 % Allowed : 17.56 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.18), residues: 2370 helix: 1.69 (0.29), residues: 399 sheet: 0.26 (0.17), residues: 879 loop : -0.83 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 47 HIS 0.003 0.001 HIS I 77 PHE 0.023 0.002 PHE E 383 TYR 0.008 0.001 TYR E 384 ARG 0.009 0.000 ARG A 500 *********************** 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 247 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 169 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7520 (t0) cc_final: 0.7136 (t0) REVERT: B 588 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7395 (mmm160) REVERT: B 655 LYS cc_start: 0.8034 (tptt) cc_final: 0.6941 (mtmt) REVERT: C 129 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.8974 (mt) REVERT: C 430 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8361 (pt) REVERT: C 457 ASP cc_start: 0.7540 (t0) cc_final: 0.7338 (t0) REVERT: C 478 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7663 (m110) REVERT: D 540 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7641 (mp-120) REVERT: D 542 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7302 (mtp85) REVERT: D 588 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7275 (mmm160) REVERT: F 540 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7794 (mp-120) REVERT: G 80 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.3667 (mm) REVERT: I 35 ASN cc_start: 0.5897 (OUTLIER) cc_final: 0.5347 (t0) outliers start: 78 outliers final: 65 residues processed: 235 average time/residue: 0.3383 time to fit residues: 121.8935 Evaluate side-chains 241 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER 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 129 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 128 THR 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 202 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 513 VAL 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 G residue 100 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 190 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20469 Z= 0.362 Angle : 0.652 12.685 27804 Z= 0.327 Chirality : 0.047 0.269 3342 Planarity : 0.004 0.056 3438 Dihedral : 5.572 54.597 4263 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.59 % Allowed : 17.89 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2370 helix: 1.19 (0.28), residues: 420 sheet: 0.32 (0.17), residues: 852 loop : -0.98 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS C 374 PHE 0.026 0.002 PHE C 383 TYR 0.011 0.001 TYR E 384 ARG 0.009 0.000 ARG A 500 ********************** 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 244 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 168 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ASP cc_start: 0.7560 (t0) cc_final: 0.7285 (t0) REVERT: B 588 ARG cc_start: 0.8054 (ttp-170) cc_final: 0.7423 (mmm160) REVERT: B 655 LYS cc_start: 0.8032 (tptt) cc_final: 0.7010 (mtmt) REVERT: C 430 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8354 (pt) REVERT: C 478 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7711 (m110) REVERT: D 540 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7588 (mp-120) REVERT: D 542 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7329 (mtp85) REVERT: D 588 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7327 (mmm160) REVERT: F 540 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7759 (mp-120) REVERT: G 48 MET cc_start: 0.7078 (ptp) cc_final: 0.6621 (pmm) REVERT: G 80 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.3770 (mm) REVERT: I 35 ASN cc_start: 0.5941 (OUTLIER) cc_final: 0.5348 (t0) REVERT: K 48 MET cc_start: 0.7285 (ptp) cc_final: 0.6652 (pmm) outliers start: 76 outliers final: 66 residues processed: 234 average time/residue: 0.3254 time to fit residues: 118.4418 Evaluate side-chains 240 residues out of total 2118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER 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 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 225 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 128 THR 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 202 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 513 VAL 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 G residue 80 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 35 ASN Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain K residue 80 LEU Chi-restraints excluded: chain K residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.3980 chunk 202 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 195 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.199863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139339 restraints weight = 22480.627| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.35 r_work: 0.2953 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20469 Z= 0.179 Angle : 0.534 11.240 27804 Z= 0.274 Chirality : 0.043 0.263 3342 Planarity : 0.004 0.051 3438 Dihedral : 5.074 50.858 4263 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.07 % Allowed : 18.32 % Favored : 78.61 % 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: 0.05 (0.18), residues: 2370 helix: 1.77 (0.29), residues: 402 sheet: 0.32 (0.17), residues: 879 loop : -0.83 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 427 HIS 0.003 0.001 HIS I 77 PHE 0.016 0.001 PHE E 383 TYR 0.010 0.001 TYR A 173 ARG 0.009 0.000 ARG A 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.47 seconds wall clock time: 82 minutes 11.15 seconds (4931.15 seconds total)