Starting phenix.real_space_refine on Fri Feb 16 16:05:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ki4_22884/02_2024/7ki4_22884.pdb" } resolution = 2.9 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= 0.003 sd= 0.087 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 78 5.16 5 C 9978 2.51 5 N 2553 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 279": "NH1" <-> "NH2" Residue "E PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 452": "OD1" <-> "OD2" Residue "E TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15738 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3404 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 790 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "U" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} 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: 9.51, per 1000 atoms: 0.60 Number of scatterers: 15738 At special positions: 0 Unit cell: (111.3, 113.4, 152.25, 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 78 16.00 O 3129 8.00 N 2553 7.00 C 9978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.02 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA Q 3 " - " MAN Q 4 " " BMA U 3 " - " MAN U 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA Q 3 " - " MAN Q 5 " " BMA U 3 " - " MAN U 5 " BETA1-4 " 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " BETA1-6 " NAG M 1 " - " FUC M 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 6 " " NAG U 1 " - " FUC U 6 " NAG-ASN " NAG I 1 " - " ASN A 99 " " NAG J 1 " - " ASN A 464 " " NAG K 1 " - " ASN A 414 " " NAG M 1 " - " ASN A 67 " " NAG N 1 " - " ASN B 99 " " NAG O 1 " - " ASN B 464 " " NAG P 1 " - " ASN B 414 " " NAG Q 1 " - " ASN B 67 " " NAG R 1 " - " ASN E 99 " " NAG S 1 " - " ASN E 464 " " NAG T 1 " - " ASN E 414 " " NAG U 1 " - " ASN E 67 " Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 3.1 seconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 33 sheets defined 30.3% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.628A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.062A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 187' Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.323A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY A 442 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 3.627A pdb=" N SER B 69 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 4.061A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.322A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY B 442 " --> pdb=" O TYR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.627A pdb=" N SER E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.537A pdb=" N ILE E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 4.061A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.896A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 154 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 184 through 187 removed outlier: 3.504A pdb=" N ILE E 187 " --> pdb=" O VAL E 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 184 through 187' Processing helix chain 'E' and resid 191 through 215 removed outlier: 4.323A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 437 through 442 removed outlier: 4.320A pdb=" N GLY E 442 " --> pdb=" O TYR E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 481 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.537A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 10.218A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.574A pdb=" N MET A 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.385A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N TYR H 93 " --> pdb=" O TRP H 109 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TRP H 109 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS H 95 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG H 97 " --> pdb=" O GLY H 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 162 removed outlier: 10.219A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.994A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG B 365 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AC1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.386A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.900A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N TYR D 93 " --> pdb=" O TRP D 109 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N TRP D 109 " --> pdb=" O TYR D 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS D 95 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA D 107 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 97 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY D 105 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.900A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 162 removed outlier: 10.218A pdb=" N THR E 168 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP E 56 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC8, first strand: chain 'E' and resid 226 through 227 removed outlier: 3.795A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 263 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE E 277 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 9.995A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 303 removed outlier: 5.938A pdb=" N ARG E 365 " --> pdb=" O VAL E 449 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.385A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N TYR G 93 " --> pdb=" O TRP G 109 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N TRP G 109 " --> pdb=" O TYR G 93 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N CYS G 95 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ALA G 107 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG G 97 " --> pdb=" O GLY G 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY G 105 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2001 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: 6.07 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3758 1.33 - 1.46: 4468 1.46 - 1.59: 7656 1.59 - 1.72: 18 1.72 - 1.85: 114 Bond restraints: 16014 Sorted by residual: bond pdb=" CB ILE B 27 " pdb=" CG1 ILE B 27 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CB ILE A 27 " pdb=" CG1 ILE A 27 " ideal model delta sigma weight residual 1.530 1.609 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" CB ILE E 27 " pdb=" CG1 ILE E 27 " ideal model delta sigma weight residual 1.530 1.608 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CA ASP A 188 " pdb=" C ASP A 188 " ideal model delta sigma weight residual 1.526 1.575 -0.049 1.28e-02 6.10e+03 1.48e+01 bond pdb=" CB LEU B 481 " pdb=" CG LEU B 481 " ideal model delta sigma weight residual 1.530 1.607 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 16009 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.47: 417 106.47 - 113.35: 8833 113.35 - 120.23: 5865 120.23 - 127.11: 6569 127.11 - 133.99: 96 Bond angle restraints: 21780 Sorted by residual: angle pdb=" C GLN D 39 " pdb=" N PRO D 40 " pdb=" CA PRO D 40 " ideal model delta sigma weight residual 119.66 125.84 -6.18 7.30e-01 1.88e+00 7.16e+01 angle pdb=" C GLN H 39 " pdb=" N PRO H 40 " pdb=" CA PRO H 40 " ideal model delta sigma weight residual 119.66 125.83 -6.17 7.30e-01 1.88e+00 7.15e+01 angle pdb=" C GLN G 39 " pdb=" N PRO G 40 " pdb=" CA PRO G 40 " ideal model delta sigma weight residual 119.66 125.80 -6.14 7.30e-01 1.88e+00 7.08e+01 angle pdb=" N LYS A 189 " pdb=" CA LYS A 189 " pdb=" C LYS A 189 " ideal model delta sigma weight residual 113.55 103.30 10.25 1.26e+00 6.30e-01 6.62e+01 angle pdb=" N LYS B 189 " pdb=" CA LYS B 189 " pdb=" C LYS B 189 " ideal model delta sigma weight residual 113.55 103.31 10.24 1.26e+00 6.30e-01 6.61e+01 ... (remaining 21775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 9771 21.48 - 42.95: 198 42.95 - 64.43: 63 64.43 - 85.90: 54 85.90 - 107.38: 24 Dihedral angle restraints: 10110 sinusoidal: 4293 harmonic: 5817 Sorted by residual: dihedral pdb=" O4 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C5 BMA U 3 " pdb=" O5 BMA U 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.64 107.35 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1716 0.076 - 0.152: 697 0.152 - 0.229: 206 0.229 - 0.305: 48 0.305 - 0.381: 18 Chirality restraints: 2685 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.89e+01 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.87e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.85e+01 ... (remaining 2682 not shown) Planarity restraints: 2715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 67 " -0.051 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" CG ASN E 67 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 67 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E 67 " 0.076 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " 0.051 2.00e-02 2.50e+03 5.10e-02 3.25e+01 pdb=" CG ASN A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 67 " 0.051 2.00e-02 2.50e+03 5.09e-02 3.24e+01 pdb=" CG ASN B 67 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 67 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.062 2.00e-02 2.50e+03 ... (remaining 2712 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5260 2.87 - 3.38: 14474 3.38 - 3.88: 27386 3.88 - 4.39: 31469 4.39 - 4.90: 52563 Nonbonded interactions: 131152 Sorted by model distance: nonbonded pdb=" O ASP B 188 " pdb=" OD1 ASP B 188 " model vdw 2.361 3.040 nonbonded pdb=" O ASP A 188 " pdb=" OD1 ASP A 188 " model vdw 2.361 3.040 nonbonded pdb=" O ASP E 188 " pdb=" OD1 ASP E 188 " model vdw 2.361 3.040 nonbonded pdb=" OH TYR L 32 " pdb=" O ILE B 187 " model vdw 2.438 2.440 nonbonded pdb=" OH TYR C 32 " pdb=" O ILE E 187 " model vdw 2.438 2.440 ... (remaining 131147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } 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: 2.900 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: 0.010 Extract box with map and model: 10.940 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 47.650 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.085 16014 Z= 0.848 Angle : 1.372 10.249 21780 Z= 0.914 Chirality : 0.094 0.381 2685 Planarity : 0.006 0.042 2703 Dihedral : 13.468 107.380 6327 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.57 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.58 (0.18), residues: 1986 helix: 0.03 (0.21), residues: 456 sheet: 0.90 (0.21), residues: 561 loop : 0.43 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP D 47 HIS 0.005 0.001 HIS F 90 PHE 0.023 0.004 PHE B 253 TYR 0.048 0.005 TYR F 32 ARG 0.004 0.001 ARG E 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.816 Fit side-chains REVERT: A 205 LYS cc_start: 0.8454 (tptp) cc_final: 0.8177 (tptp) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 1.0991 time to fit residues: 467.4688 Evaluate side-chains 195 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 224 ASN L 90 HIS L 91 HIS H 1 GLN B 64 ASN B 224 ASN C 90 HIS D 1 GLN E 64 ASN E 224 ASN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16014 Z= 0.251 Angle : 0.629 8.860 21780 Z= 0.325 Chirality : 0.051 0.448 2685 Planarity : 0.004 0.038 2703 Dihedral : 9.351 65.757 2928 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.61 % Favored : 98.24 % Rotamer: Outliers : 4.04 % Allowed : 10.19 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.92 (0.19), residues: 1986 helix: 1.38 (0.24), residues: 471 sheet: 0.93 (0.21), residues: 579 loop : 0.10 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.016 0.002 PHE E 253 TYR 0.031 0.002 TYR F 32 ARG 0.006 0.001 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 232 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7265 (mttt) REVERT: A 240 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: A 244 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.7256 (ttp-110) REVERT: B 142 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: B 240 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: E 240 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: F 11 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6708 (tp) outliers start: 67 outliers final: 25 residues processed: 267 average time/residue: 1.1855 time to fit residues: 352.8494 Evaluate side-chains 224 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 120 optimal weight: 0.0070 chunk 48 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN B 393 GLN B 469 GLN D 1 GLN E 469 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16014 Z= 0.301 Angle : 0.603 8.363 21780 Z= 0.308 Chirality : 0.049 0.306 2685 Planarity : 0.005 0.046 2703 Dihedral : 7.151 46.268 2928 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.52 % Allowed : 12.06 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.70 (0.19), residues: 1986 helix: 1.55 (0.24), residues: 486 sheet: 0.69 (0.20), residues: 585 loop : -0.21 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.001 HIS L 91 PHE 0.018 0.002 PHE A 376 TYR 0.015 0.002 TYR B 239 ARG 0.006 0.001 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 210 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: A 244 ARG cc_start: 0.7573 (ttp-110) cc_final: 0.7194 (ttp-110) REVERT: B 142 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: D 72 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7625 (t0) REVERT: E 240 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: E 399 ARG cc_start: 0.6247 (ptp-110) cc_final: 0.5958 (ptp-170) REVERT: G 38 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8155 (ptt180) outliers start: 75 outliers final: 45 residues processed: 258 average time/residue: 1.1408 time to fit residues: 329.5616 Evaluate side-chains 239 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain G residue 38 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 9.9990 chunk 133 optimal weight: 0.0670 chunk 92 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 0.0050 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 0.0050 chunk 93 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 224 ASN A 393 GLN A 469 GLN H 1 GLN B 393 GLN B 469 GLN C 91 HIS D 1 GLN E 380 ASN E 469 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS G 1 GLN G 111 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16014 Z= 0.145 Angle : 0.512 6.746 21780 Z= 0.261 Chirality : 0.046 0.326 2685 Planarity : 0.004 0.044 2703 Dihedral : 5.932 38.350 2928 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.50 % Allowed : 14.29 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.87 (0.19), residues: 1986 helix: 1.87 (0.25), residues: 486 sheet: 0.71 (0.21), residues: 585 loop : -0.15 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE B 253 TYR 0.012 0.001 TYR A 239 ARG 0.003 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 1.882 Fit side-chains REVERT: A 240 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: L 90 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.8067 (p-80) REVERT: E 240 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: E 399 ARG cc_start: 0.6331 (ptp-110) cc_final: 0.6071 (ptp-170) REVERT: G 38 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8070 (ptt180) outliers start: 58 outliers final: 25 residues processed: 244 average time/residue: 1.1220 time to fit residues: 312.4247 Evaluate side-chains 211 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN A 469 GLN H 1 GLN B 393 GLN B 459 GLN B 469 GLN E 393 GLN G 1 GLN G 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16014 Z= 0.372 Angle : 0.626 9.320 21780 Z= 0.314 Chirality : 0.050 0.334 2685 Planarity : 0.005 0.042 2703 Dihedral : 5.901 34.383 2928 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.80 % Allowed : 14.77 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.58 (0.19), residues: 1986 helix: 1.68 (0.24), residues: 486 sheet: 0.51 (0.21), residues: 582 loop : -0.34 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 47 HIS 0.012 0.002 HIS F 91 PHE 0.014 0.002 PHE A 376 TYR 0.019 0.002 TYR F 32 ARG 0.004 0.001 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 178 time to evaluate : 1.937 Fit side-chains REVERT: A 82 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7955 (tmt-80) REVERT: A 240 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: B 138 MET cc_start: 0.6662 (mmm) cc_final: 0.6393 (mmm) REVERT: E 240 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: E 399 ARG cc_start: 0.6391 (ptp-110) cc_final: 0.6102 (ptp-170) REVERT: G 38 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8182 (ptt180) REVERT: G 66 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7706 (mtm180) outliers start: 63 outliers final: 41 residues processed: 223 average time/residue: 1.0737 time to fit residues: 270.4567 Evaluate side-chains 211 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 224 ASN A 393 GLN H 1 GLN B 469 GLN D 1 GLN G 1 GLN G 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16014 Z= 0.278 Angle : 0.567 9.047 21780 Z= 0.286 Chirality : 0.048 0.339 2685 Planarity : 0.004 0.041 2703 Dihedral : 5.665 31.347 2928 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.62 % Allowed : 15.13 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.52 (0.19), residues: 1986 helix: 1.70 (0.24), residues: 486 sheet: 0.44 (0.21), residues: 582 loop : -0.39 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 47 HIS 0.007 0.001 HIS F 91 PHE 0.016 0.001 PHE E 330 TYR 0.015 0.002 TYR A 239 ARG 0.004 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 1.783 Fit side-chains REVERT: A 82 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7968 (tmt-80) REVERT: A 240 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: A 406 GLU cc_start: 0.7464 (pm20) cc_final: 0.7254 (pm20) REVERT: L 90 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8254 (p-80) REVERT: B 240 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: D 38 ARG cc_start: 0.8312 (ptt180) cc_final: 0.7981 (ptt180) REVERT: D 72 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7653 (t70) REVERT: E 240 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: E 399 ARG cc_start: 0.6302 (ptp-110) cc_final: 0.6068 (ptp-170) REVERT: G 38 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8196 (ptt180) REVERT: G 66 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7714 (mtm110) outliers start: 60 outliers final: 34 residues processed: 227 average time/residue: 1.0587 time to fit residues: 270.9164 Evaluate side-chains 218 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN G 1 GLN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16014 Z= 0.254 Angle : 0.560 8.627 21780 Z= 0.283 Chirality : 0.047 0.329 2685 Planarity : 0.004 0.042 2703 Dihedral : 5.565 29.143 2928 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.74 % Allowed : 15.61 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.51 (0.19), residues: 1986 helix: 1.72 (0.24), residues: 486 sheet: 0.38 (0.21), residues: 585 loop : -0.37 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 47 HIS 0.006 0.001 HIS F 91 PHE 0.016 0.001 PHE E 330 TYR 0.015 0.001 TYR A 239 ARG 0.005 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 190 time to evaluate : 1.822 Fit side-chains REVERT: A 82 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7965 (tmt-80) REVERT: A 240 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: A 406 GLU cc_start: 0.7446 (pm20) cc_final: 0.7203 (pm20) REVERT: L 90 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.8296 (p-80) REVERT: B 138 MET cc_start: 0.6634 (mmm) cc_final: 0.6393 (mmm) REVERT: B 240 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: C 52 LYS cc_start: 0.8393 (ptmm) cc_final: 0.8121 (ptmt) REVERT: D 72 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7624 (t70) REVERT: E 219 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6797 (pt0) REVERT: E 240 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: E 399 ARG cc_start: 0.6295 (ptp-110) cc_final: 0.6066 (ptp-170) REVERT: G 38 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8263 (ptt180) REVERT: G 66 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7710 (mtm110) outliers start: 62 outliers final: 39 residues processed: 234 average time/residue: 1.0334 time to fit residues: 277.3486 Evaluate side-chains 233 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 119 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16014 Z= 0.182 Angle : 0.524 7.886 21780 Z= 0.266 Chirality : 0.046 0.328 2685 Planarity : 0.004 0.043 2703 Dihedral : 5.256 26.970 2928 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.25 % Allowed : 16.64 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.63 (0.19), residues: 1986 helix: 1.85 (0.24), residues: 486 sheet: 0.51 (0.21), residues: 597 loop : -0.39 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 47 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.001 PHE E 330 TYR 0.013 0.001 TYR A 239 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 2.138 Fit side-chains REVERT: A 82 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7932 (tmt-80) REVERT: A 406 GLU cc_start: 0.7447 (pm20) cc_final: 0.7228 (pm20) REVERT: L 90 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8290 (p-80) REVERT: B 138 MET cc_start: 0.6613 (mmm) cc_final: 0.6349 (mmm) REVERT: B 240 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: D 1 GLN cc_start: 0.7435 (pt0) cc_final: 0.6913 (pt0) REVERT: E 240 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: E 399 ARG cc_start: 0.6297 (ptp-110) cc_final: 0.6089 (ptp-170) REVERT: G 38 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8174 (ptt180) outliers start: 54 outliers final: 39 residues processed: 237 average time/residue: 1.0054 time to fit residues: 270.0701 Evaluate side-chains 239 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 64 MET Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 137 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 393 GLN L 79 GLN H 1 GLN B 393 GLN G 1 GLN G 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16014 Z= 0.277 Angle : 0.571 8.449 21780 Z= 0.288 Chirality : 0.047 0.328 2685 Planarity : 0.004 0.042 2703 Dihedral : 5.443 32.358 2928 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 3.44 % Allowed : 16.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.54 (0.19), residues: 1986 helix: 1.79 (0.24), residues: 486 sheet: 0.37 (0.21), residues: 585 loop : -0.37 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 47 HIS 0.007 0.001 HIS C 91 PHE 0.016 0.001 PHE E 330 TYR 0.018 0.001 TYR A 239 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 1.732 Fit side-chains REVERT: A 82 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7970 (tmt-80) REVERT: A 406 GLU cc_start: 0.7482 (pm20) cc_final: 0.7259 (pm20) REVERT: B 138 MET cc_start: 0.6667 (mmm) cc_final: 0.6406 (mmm) REVERT: B 240 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: E 219 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: E 240 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: G 38 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8226 (ptt180) outliers start: 57 outliers final: 41 residues processed: 233 average time/residue: 0.9407 time to fit residues: 249.9514 Evaluate side-chains 230 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 184 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN H 1 GLN D 1 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16014 Z= 0.251 Angle : 0.556 8.497 21780 Z= 0.280 Chirality : 0.047 0.334 2685 Planarity : 0.004 0.043 2703 Dihedral : 5.442 37.715 2928 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.89 % Allowed : 17.30 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.19), residues: 1986 helix: 1.78 (0.24), residues: 486 sheet: 0.42 (0.21), residues: 597 loop : -0.40 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 47 HIS 0.006 0.001 HIS C 91 PHE 0.016 0.001 PHE E 330 TYR 0.015 0.001 TYR A 239 ARG 0.006 0.000 ARG F 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 1.864 Fit side-chains REVERT: A 82 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7937 (tmt-80) REVERT: A 406 GLU cc_start: 0.7510 (pm20) cc_final: 0.7266 (pm20) REVERT: B 240 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6999 (tm-30) REVERT: E 219 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6786 (pt0) REVERT: E 240 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: G 38 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8218 (ptt180) outliers start: 48 outliers final: 37 residues processed: 224 average time/residue: 0.9977 time to fit residues: 257.0138 Evaluate side-chains 229 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 392 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 142 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 159 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 224 ASN A 393 GLN H 1 GLN B 459 GLN D 1 GLN ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN G 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117529 restraints weight = 19966.748| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.04 r_work: 0.3339 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16014 Z= 0.146 Angle : 0.503 6.795 21780 Z= 0.256 Chirality : 0.045 0.318 2685 Planarity : 0.004 0.043 2703 Dihedral : 4.997 27.986 2928 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.05 % Allowed : 18.08 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.75 (0.19), residues: 1986 helix: 1.92 (0.24), residues: 486 sheet: 0.61 (0.21), residues: 597 loop : -0.32 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.003 0.001 HIS F 90 PHE 0.016 0.001 PHE E 330 TYR 0.011 0.001 TYR A 239 ARG 0.006 0.000 ARG F 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5544.48 seconds wall clock time: 99 minutes 42.46 seconds (5982.46 seconds total)