Starting phenix.real_space_refine on Thu Mar 5 16:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlk_14783/03_2026/7zlk_14783.map" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 14758 2.51 5 N 3941 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23518 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 954 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "Q" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "T" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" 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: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.31, per 1000 atoms: 0.23 Number of scatterers: 23518 At special positions: 0 Unit cell: (151.8, 151.8, 170.2, 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 141 16.00 O 4678 8.00 N 3941 7.00 C 14758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.19 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.02 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 86 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 7 " " MAN J 4 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 7 " " MAN c 4 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " " BMA K 3 " - " MAN K 4 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 188 " " NAG A 605 " - " ASN A 362 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 188 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 88 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 241 " " NAG D 604 " - " ASN D 289 " " NAG D 605 " - " ASN D 189 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 386 " " NAG D 608 " - " ASN D 88 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 448 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 301 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 19.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.044A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.053A pdb=" N ARG A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.995A pdb=" N GLN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 545 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 569 through 596 removed outlier: 5.482A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 631 through 649 removed outlier: 4.014A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.566A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.293A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 535 Processing helix chain 'E' and resid 536 through 545 removed outlier: 3.614A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.611A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.889A pdb=" N LYS D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.516A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 543 through 550 removed outlier: 3.879A pdb=" N VAL F 549 " --> pdb=" O LEU F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 556 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 652 through 662 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.599A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.648A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 77 through 81 Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.503A pdb=" N HIS S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 5.733A pdb=" N SER S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.298A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.917A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.860A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.170A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 310 removed outlier: 6.929A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.760A pdb=" N ARG C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.350A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.876A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 416 Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 310 removed outlier: 6.724A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.251A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.801A pdb=" N ARG D 66 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.714A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.614A pdb=" N HIS D 374 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.762A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.951A pdb=" N TYR M 33 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.078A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 8 through 11 removed outlier: 6.559A pdb=" N TRP N 33 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AE3, first strand: chain 'N' and resid 17 through 22 Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 8 Processing sheet with id=AE5, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.948A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.755A pdb=" N TRP Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.581A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'S' and resid 57 through 59 removed outlier: 6.677A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR S 33 " --> pdb=" O GLU S 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.606A pdb=" N TRP T 33 " --> pdb=" O VAL T 45 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 8 through 11 Processing sheet with id=AF9, first strand: chain 'T' and resid 17 through 22 889 hydrogen bonds defined for protein. 2214 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: 5.87 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4525 1.32 - 1.46: 8381 1.46 - 1.60: 10899 1.60 - 1.75: 41 1.75 - 1.89: 181 Bond restraints: 24027 Sorted by residual: bond pdb=" N PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" CB HIS D 308 " pdb=" CG HIS D 308 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.29e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" CB LEU T 107 " pdb=" CG LEU T 107 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PHE Q 29 " pdb=" CG PHE Q 29 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 ... (remaining 24022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.10: 32374 6.10 - 12.20: 285 12.20 - 18.30: 8 18.30 - 24.40: 0 24.40 - 30.51: 1 Bond angle restraints: 32668 Sorted by residual: angle pdb=" N ASP S 101 " pdb=" CA ASP S 101 " pdb=" C ASP S 101 " ideal model delta sigma weight residual 109.81 140.32 -30.51 2.21e+00 2.05e-01 1.91e+02 angle pdb=" N PHE Q 29 " pdb=" CA PHE Q 29 " pdb=" C PHE Q 29 " ideal model delta sigma weight residual 113.02 127.64 -14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" N PHE H 29 " pdb=" CA PHE H 29 " pdb=" C PHE H 29 " ideal model delta sigma weight residual 113.02 126.23 -13.21 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N THR P 92 " pdb=" CA THR P 92 " pdb=" C THR P 92 " ideal model delta sigma weight residual 111.36 122.50 -11.14 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N PRO S 102 " pdb=" CA PRO S 102 " pdb=" C PRO S 102 " ideal model delta sigma weight residual 113.40 100.56 12.84 1.34e+00 5.57e-01 9.18e+01 ... (remaining 32663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 14997 21.69 - 43.38: 361 43.38 - 65.07: 100 65.07 - 86.76: 108 86.76 - 108.45: 57 Dihedral angle restraints: 15623 sinusoidal: 7453 harmonic: 8170 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -164.40 78.40 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -163.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -140.56 54.56 1 1.00e+01 1.00e-02 4.03e+01 ... (remaining 15620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3091 0.141 - 0.283: 659 0.283 - 0.424: 152 0.424 - 0.565: 42 0.565 - 0.707: 2 Chirality restraints: 3946 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 3943 not shown) Planarity restraints: 4037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.314 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG b 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 608 " 0.254 2.00e-02 2.50e+03 2.10e-01 5.53e+02 pdb=" C7 NAG D 608 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG D 608 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 608 " -0.347 2.00e-02 2.50e+03 pdb=" O7 NAG D 608 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 603 " 0.225 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG D 603 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 603 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG D 603 " -0.315 2.00e-02 2.50e+03 pdb=" O7 NAG D 603 " 0.176 2.00e-02 2.50e+03 ... (remaining 4034 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7414 2.86 - 3.37: 21544 3.37 - 3.88: 39653 3.88 - 4.39: 45561 4.39 - 4.90: 72660 Nonbonded interactions: 186832 Sorted by model distance: nonbonded pdb=" O PHE S 100H" pdb=" NE1 TRP S 103 " model vdw 2.348 3.120 nonbonded pdb=" N ALA F 541 " pdb=" O ALA F 541 " model vdw 2.357 2.496 nonbonded pdb=" N ALA B 533 " pdb=" N SER B 534 " model vdw 2.375 2.560 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 429 " model vdw 2.380 3.120 nonbonded pdb=" NZ LYS D 500 " pdb=" OD2 ASP N 51 " model vdw 2.394 3.120 ... (remaining 186827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 35 through 605) selection = (chain 'D' and resid 35 through 605) } ncs_group { reference = (chain 'B' and (resid 523 through 558 or resid 569 through 651)) selection = (chain 'E' and resid 523 through 651) selection = (chain 'F' and resid 523 through 651) } ncs_group { reference = chain 'G' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 7)) selection = (chain 'X' and (resid 1 or resid 4 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 7)) selection = (chain 'd' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'M' and resid 1 through 108) selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } 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 group one per residue 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.960 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.022 0.155 24168 Z= 1.154 Angle : 1.889 30.506 33048 Z= 1.219 Chirality : 0.131 0.707 3946 Planarity : 0.011 0.273 4000 Dihedral : 14.463 108.451 10232 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.15), residues: 2780 helix: -0.23 (0.23), residues: 387 sheet: 0.75 (0.16), residues: 844 loop : 0.16 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 469 TYR 0.062 0.009 TYR T 48 PHE 0.050 0.007 PHE M 52 TRP 0.067 0.011 TRP O 47 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02141 (24027) covalent geometry : angle 1.84932 (32668) SS BOND : bond 0.02853 ( 43) SS BOND : angle 3.16760 ( 86) hydrogen bonds : bond 0.16644 ( 842) hydrogen bonds : angle 7.63685 ( 2214) link_ALPHA1-2 : bond 0.08518 ( 1) link_ALPHA1-2 : angle 7.57404 ( 3) link_ALPHA1-3 : bond 0.08828 ( 15) link_ALPHA1-3 : angle 5.33909 ( 45) link_ALPHA1-6 : bond 0.05772 ( 16) link_ALPHA1-6 : angle 3.21648 ( 48) link_BETA1-4 : bond 0.07357 ( 29) link_BETA1-4 : angle 5.36914 ( 87) link_NAG-ASN : bond 0.07577 ( 37) link_NAG-ASN : angle 2.84058 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 872 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8654 (t) cc_final: 0.8402 (p) REVERT: A 78 ASP cc_start: 0.8378 (m-30) cc_final: 0.7793 (t70) REVERT: A 95 MET cc_start: 0.8766 (ptt) cc_final: 0.8552 (ppp) REVERT: A 180 ASP cc_start: 0.8380 (m-30) cc_final: 0.8171 (m-30) REVERT: A 284 ILE cc_start: 0.8443 (mt) cc_final: 0.8047 (tt) REVERT: A 368 ASP cc_start: 0.8253 (t0) cc_final: 0.7971 (t0) REVERT: A 387 THR cc_start: 0.8315 (p) cc_final: 0.8027 (t) REVERT: A 426 MET cc_start: 0.6826 (mtp) cc_final: 0.6426 (mtm) REVERT: B 523 LEU cc_start: 0.8850 (mt) cc_final: 0.8550 (mt) REVERT: B 530 MET cc_start: 0.3290 (mmp) cc_final: 0.2890 (mmp) REVERT: B 624 ASN cc_start: 0.6565 (m-40) cc_final: 0.5289 (t0) REVERT: B 631 TRP cc_start: 0.6428 (m-10) cc_final: 0.6209 (m-10) REVERT: C 42 VAL cc_start: 0.9391 (t) cc_final: 0.9187 (p) REVERT: C 68 VAL cc_start: 0.9051 (p) cc_final: 0.8729 (p) REVERT: C 103 GLN cc_start: 0.8420 (tp40) cc_final: 0.7819 (tm-30) REVERT: C 165 ILE cc_start: 0.8294 (mt) cc_final: 0.8026 (mm) REVERT: C 370 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7836 (mp0) REVERT: C 419 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7883 (mtp180) REVERT: E 530 MET cc_start: 0.8202 (mtp) cc_final: 0.7730 (mtm) REVERT: E 601 LYS cc_start: 0.8309 (mttt) cc_final: 0.7624 (mtmt) REVERT: E 618 SER cc_start: 0.8218 (m) cc_final: 0.7983 (p) REVERT: E 639 THR cc_start: 0.8432 (m) cc_final: 0.7565 (t) REVERT: E 644 ASN cc_start: 0.8448 (m-40) cc_final: 0.8171 (t0) REVERT: E 648 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8212 (mt-10) REVERT: D 92 ASN cc_start: 0.7693 (t0) cc_final: 0.7463 (t0) REVERT: D 198 THR cc_start: 0.8509 (m) cc_final: 0.8256 (p) REVERT: D 246 GLN cc_start: 0.7241 (mp10) cc_final: 0.5895 (tp40) REVERT: D 434 MET cc_start: 0.8221 (ttm) cc_final: 0.7993 (ttp) REVERT: D 468 PHE cc_start: 0.7609 (m-80) cc_final: 0.6957 (m-80) REVERT: F 540 GLN cc_start: 0.8985 (tp40) cc_final: 0.8490 (tp40) REVERT: F 545 LEU cc_start: 0.9009 (tp) cc_final: 0.8491 (tt) REVERT: F 601 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8716 (mmtp) REVERT: F 623 TRP cc_start: 0.9149 (m100) cc_final: 0.8679 (m100) REVERT: H 81 LYS cc_start: 0.8180 (tttt) cc_final: 0.7917 (mmtm) REVERT: H 82 MET cc_start: 0.6850 (tpp) cc_final: 0.6323 (tpp) REVERT: H 93 VAL cc_start: 0.8808 (t) cc_final: 0.8207 (m) REVERT: H 110 LEU cc_start: 0.8435 (tp) cc_final: 0.8227 (tp) REVERT: L 27 GLN cc_start: 0.7333 (tp-100) cc_final: 0.7044 (tm-30) REVERT: L 27 LEU cc_start: 0.8126 (mt) cc_final: 0.7793 (mt) REVERT: L 61 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: L 97 THR cc_start: 0.8924 (t) cc_final: 0.8682 (t) REVERT: M 72 ASP cc_start: 0.7924 (t0) cc_final: 0.7412 (t0) REVERT: M 86 ASP cc_start: 0.8215 (m-30) cc_final: 0.7948 (m-30) REVERT: M 91 TYR cc_start: 0.7775 (m-80) cc_final: 0.7539 (m-80) REVERT: M 100 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8374 (tt0) REVERT: N 44 LEU cc_start: 0.6950 (tp) cc_final: 0.6717 (tp) REVERT: N 49 ASP cc_start: 0.8065 (m-30) cc_final: 0.7801 (m-30) REVERT: N 52 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7201 (mtp-110) REVERT: N 60 PHE cc_start: 0.7893 (m-80) cc_final: 0.7236 (m-80) REVERT: N 70 THR cc_start: 0.8612 (m) cc_final: 0.8336 (t) REVERT: N 81 GLU cc_start: 0.8825 (tt0) cc_final: 0.8517 (mm-30) REVERT: N 83 ASP cc_start: 0.7982 (m-30) cc_final: 0.7403 (p0) REVERT: N 87 GLN cc_start: 0.8709 (tt0) cc_final: 0.8287 (tt0) REVERT: N 93 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8442 (ttp-110) REVERT: N 94 ASP cc_start: 0.8326 (m-30) cc_final: 0.7899 (m-30) REVERT: O 6 GLN cc_start: 0.7551 (pt0) cc_final: 0.6692 (pt0) REVERT: O 59 TYR cc_start: 0.6178 (m-80) cc_final: 0.5782 (m-80) REVERT: O 82 MET cc_start: 0.6546 (mtp) cc_final: 0.5871 (mmm) REVERT: O 100 MET cc_start: 0.8657 (mtp) cc_final: 0.7665 (ttm) REVERT: O 105 HIS cc_start: 0.7594 (p-80) cc_final: 0.7289 (m-70) REVERT: P 27 GLN cc_start: 0.6966 (mt0) cc_final: 0.6747 (mp10) REVERT: P 51 ILE cc_start: 0.7580 (mm) cc_final: 0.7349 (mm) REVERT: P 71 PHE cc_start: 0.8016 (m-80) cc_final: 0.7583 (m-10) REVERT: P 100 GLN cc_start: 0.7358 (pm20) cc_final: 0.7017 (pm20) REVERT: Q 36 TRP cc_start: 0.8691 (m100) cc_final: 0.7928 (m100) REVERT: Q 93 VAL cc_start: 0.9275 (t) cc_final: 0.9059 (m) REVERT: Q 100 MET cc_start: 0.8336 (mtp) cc_final: 0.7800 (mmt) REVERT: R 27 HIS cc_start: 0.8061 (t-90) cc_final: 0.7614 (t70) REVERT: R 38 GLN cc_start: 0.8105 (tt0) cc_final: 0.7692 (tm-30) REVERT: S 4 LEU cc_start: 0.8282 (mt) cc_final: 0.7907 (mp) REVERT: S 24 VAL cc_start: 0.8303 (t) cc_final: 0.7097 (t) REVERT: S 37 ILE cc_start: 0.7477 (mt) cc_final: 0.6989 (mm) REVERT: S 58 ASN cc_start: 0.7426 (t0) cc_final: 0.7120 (t0) REVERT: S 72 ASP cc_start: 0.7284 (t0) cc_final: 0.7042 (t0) REVERT: S 75 LYS cc_start: 0.8982 (mttt) cc_final: 0.8764 (mtmm) REVERT: S 78 PHE cc_start: 0.5581 (m-80) cc_final: 0.4675 (m-80) REVERT: S 107 THR cc_start: 0.8256 (t) cc_final: 0.7964 (p) REVERT: T 45 VAL cc_start: 0.8098 (t) cc_final: 0.7665 (t) outliers start: 2 outliers final: 1 residues processed: 874 average time/residue: 0.1827 time to fit residues: 235.0609 Evaluate side-chains 441 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN B 577 GLN C 195 ASN C 249 HIS C 425 ASN E 616 ASN E 653 GLN D 94 ASN D 203 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 553 ASN F 653 GLN H 6 GLN L 37 GLN ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 35 GLN O 100 HIS P 17 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100CASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.114389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086479 restraints weight = 64430.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.089113 restraints weight = 38870.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.089825 restraints weight = 25951.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090257 restraints weight = 24469.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090380 restraints weight = 22043.552| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24168 Z= 0.190 Angle : 0.871 19.842 33048 Z= 0.434 Chirality : 0.053 0.395 3946 Planarity : 0.006 0.058 4000 Dihedral : 12.537 83.091 5010 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.77 % Allowed : 12.05 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 2780 helix: 0.72 (0.26), residues: 391 sheet: 0.46 (0.16), residues: 896 loop : -0.05 (0.16), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 18 TYR 0.029 0.002 TYR E 643 PHE 0.036 0.003 PHE C 277 TRP 0.023 0.002 TRP B 610 HIS 0.014 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00410 (24027) covalent geometry : angle 0.82080 (32668) SS BOND : bond 0.00329 ( 43) SS BOND : angle 1.39476 ( 86) hydrogen bonds : bond 0.05801 ( 842) hydrogen bonds : angle 6.02165 ( 2214) link_ALPHA1-2 : bond 0.00773 ( 1) link_ALPHA1-2 : angle 5.78761 ( 3) link_ALPHA1-3 : bond 0.01566 ( 15) link_ALPHA1-3 : angle 2.47295 ( 45) link_ALPHA1-6 : bond 0.01048 ( 16) link_ALPHA1-6 : angle 1.66578 ( 48) link_BETA1-4 : bond 0.01600 ( 29) link_BETA1-4 : angle 4.17227 ( 87) link_NAG-ASN : bond 0.00768 ( 37) link_NAG-ASN : angle 2.84792 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 577 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8354 (m100) cc_final: 0.7680 (m100) REVERT: A 180 ASP cc_start: 0.8430 (m-30) cc_final: 0.8069 (m-30) REVERT: A 426 MET cc_start: 0.6126 (mtp) cc_final: 0.5324 (mtp) REVERT: B 530 MET cc_start: 0.2900 (mmp) cc_final: 0.2392 (mmt) REVERT: B 535 MET cc_start: 0.8416 (mmm) cc_final: 0.8196 (mmt) REVERT: B 588 ARG cc_start: 0.8924 (tmm-80) cc_final: 0.8633 (ttm-80) REVERT: B 601 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8255 (mmmm) REVERT: B 628 TRP cc_start: 0.2784 (m-10) cc_final: 0.2557 (m-10) REVERT: C 75 VAL cc_start: 0.8775 (p) cc_final: 0.8459 (m) REVERT: C 95 MET cc_start: 0.8578 (ptp) cc_final: 0.8338 (ptp) REVERT: C 112 TRP cc_start: 0.8105 (m100) cc_final: 0.7633 (m100) REVERT: C 180 ASP cc_start: 0.8810 (m-30) cc_final: 0.8480 (t0) REVERT: C 342 LEU cc_start: 0.9040 (mt) cc_final: 0.8818 (tp) REVERT: C 434 MET cc_start: 0.8930 (ttp) cc_final: 0.8619 (ttp) REVERT: E 557 ARG cc_start: 0.3682 (OUTLIER) cc_final: 0.3441 (mtt-85) REVERT: E 601 LYS cc_start: 0.8400 (mttt) cc_final: 0.7857 (mtmt) REVERT: E 618 SER cc_start: 0.7636 (m) cc_final: 0.7157 (p) REVERT: E 620 ASP cc_start: 0.8678 (p0) cc_final: 0.8342 (p0) REVERT: E 627 THR cc_start: 0.8807 (p) cc_final: 0.8579 (p) REVERT: E 631 TRP cc_start: 0.8817 (t-100) cc_final: 0.8594 (t-100) REVERT: E 639 THR cc_start: 0.8603 (m) cc_final: 0.7927 (p) REVERT: E 644 ASN cc_start: 0.8309 (m-40) cc_final: 0.8007 (m-40) REVERT: E 646 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8379 (mm) REVERT: E 647 GLU cc_start: 0.7471 (pp20) cc_final: 0.6939 (pp20) REVERT: E 648 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8193 (mt-10) REVERT: D 92 ASN cc_start: 0.7807 (t0) cc_final: 0.7581 (t0) REVERT: D 116 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8814 (mp) REVERT: D 373 MET cc_start: 0.7573 (mtm) cc_final: 0.6942 (mtp) REVERT: D 425 ASN cc_start: 0.8487 (p0) cc_final: 0.7954 (p0) REVERT: D 468 PHE cc_start: 0.7587 (m-80) cc_final: 0.7250 (m-80) REVERT: F 601 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8631 (mmmm) REVERT: F 623 TRP cc_start: 0.8680 (m100) cc_final: 0.8390 (m100) REVERT: H 36 TRP cc_start: 0.8559 (m100) cc_final: 0.7274 (m100) REVERT: H 82 MET cc_start: 0.7161 (tpp) cc_final: 0.6401 (tpp) REVERT: H 102 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.6481 (t80) REVERT: L 4 MET cc_start: 0.6645 (mtm) cc_final: 0.6289 (mtm) REVERT: L 27 GLN cc_start: 0.7510 (tp-100) cc_final: 0.6933 (tm-30) REVERT: L 27 LEU cc_start: 0.7902 (mt) cc_final: 0.7388 (mt) REVERT: L 37 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7311 (pp30) REVERT: L 49 TYR cc_start: 0.7379 (p90) cc_final: 0.6910 (p90) REVERT: L 61 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7958 (mtm-85) REVERT: L 71 PHE cc_start: 0.8611 (m-80) cc_final: 0.7990 (m-80) REVERT: L 79 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7282 (tm-30) REVERT: L 94 PHE cc_start: 0.6383 (m-80) cc_final: 0.5931 (m-80) REVERT: L 96 TRP cc_start: 0.7528 (m-90) cc_final: 0.6321 (m-90) REVERT: M 72 ASP cc_start: 0.7901 (t0) cc_final: 0.7268 (t0) REVERT: M 86 ASP cc_start: 0.8031 (m-30) cc_final: 0.7753 (m-30) REVERT: M 87 THR cc_start: 0.9506 (t) cc_final: 0.9165 (m) REVERT: M 100 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8218 (mt-10) REVERT: M 100 MET cc_start: 0.6912 (ptp) cc_final: 0.6490 (mtt) REVERT: N 24 ASN cc_start: 0.8201 (t0) cc_final: 0.7701 (t0) REVERT: N 25 ASN cc_start: 0.8222 (m-40) cc_final: 0.7880 (m110) REVERT: N 34 TYR cc_start: 0.8206 (m-80) cc_final: 0.7758 (m-10) REVERT: N 49 ASP cc_start: 0.8007 (m-30) cc_final: 0.7776 (m-30) REVERT: N 70 THR cc_start: 0.8767 (m) cc_final: 0.8516 (p) REVERT: N 71 LEU cc_start: 0.8570 (tp) cc_final: 0.8340 (tp) REVERT: N 81 GLU cc_start: 0.8599 (tt0) cc_final: 0.8061 (mt-10) REVERT: N 90 ASP cc_start: 0.8768 (t0) cc_final: 0.8131 (t0) REVERT: O 59 TYR cc_start: 0.6316 (m-80) cc_final: 0.5444 (m-80) REVERT: O 75 MET cc_start: 0.8216 (mmm) cc_final: 0.7681 (mtp) REVERT: O 81 LYS cc_start: 0.4630 (OUTLIER) cc_final: 0.4286 (mppt) REVERT: O 82 VAL cc_start: 0.8242 (m) cc_final: 0.8003 (p) REVERT: O 100 MET cc_start: 0.8670 (mtp) cc_final: 0.7663 (ttm) REVERT: P 17 GLN cc_start: 0.8687 (tt0) cc_final: 0.8226 (mm-40) REVERT: P 27 GLN cc_start: 0.7016 (mt0) cc_final: 0.6733 (mp10) REVERT: P 50 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7558 (ptmt) REVERT: P 51 ILE cc_start: 0.8577 (mm) cc_final: 0.7643 (tp) REVERT: P 61 ARG cc_start: 0.8583 (mtm-85) cc_final: 0.8279 (mtm110) REVERT: P 71 PHE cc_start: 0.7901 (m-80) cc_final: 0.7098 (m-10) REVERT: P 100 GLN cc_start: 0.7776 (pm20) cc_final: 0.6803 (tm-30) REVERT: Q 36 TRP cc_start: 0.8625 (m100) cc_final: 0.8187 (m100) REVERT: Q 38 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7511 (ptm160) REVERT: Q 46 GLU cc_start: 0.8287 (tt0) cc_final: 0.7768 (tt0) REVERT: R 27 HIS cc_start: 0.8226 (t-90) cc_final: 0.7818 (t-170) REVERT: R 51 ILE cc_start: 0.8354 (mp) cc_final: 0.8038 (mm) REVERT: R 71 PHE cc_start: 0.7961 (m-80) cc_final: 0.7028 (m-80) REVERT: R 90 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6345 (pt0) REVERT: S 24 VAL cc_start: 0.8199 (t) cc_final: 0.7441 (t) REVERT: S 37 ILE cc_start: 0.7641 (mt) cc_final: 0.7418 (mm) REVERT: S 58 ASN cc_start: 0.7542 (t0) cc_final: 0.7264 (t0) REVERT: S 72 ASP cc_start: 0.7427 (t0) cc_final: 0.6975 (t0) REVERT: S 100 VAL cc_start: 0.9358 (t) cc_final: 0.9034 (m) REVERT: T 40 GLN cc_start: 0.7927 (mp10) cc_final: 0.7708 (mm-40) REVERT: T 104 VAL cc_start: 0.9105 (t) cc_final: 0.8811 (m) outliers start: 69 outliers final: 27 residues processed: 610 average time/residue: 0.1554 time to fit residues: 145.1936 Evaluate side-chains 448 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 413 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 145 optimal weight: 0.3980 chunk 190 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 374 HIS A 425 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 425 ASN E 616 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS L 37 GLN L 90 GLN L 93 GLN M 100CASN P 53 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN S 56 ASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085001 restraints weight = 62172.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084679 restraints weight = 47518.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085881 restraints weight = 39578.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086124 restraints weight = 31853.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086326 restraints weight = 30130.891| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24168 Z= 0.225 Angle : 0.822 21.270 33048 Z= 0.406 Chirality : 0.050 0.329 3946 Planarity : 0.005 0.080 4000 Dihedral : 11.025 78.957 5006 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.98 % Allowed : 14.18 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.16), residues: 2780 helix: 0.61 (0.27), residues: 406 sheet: 0.26 (0.16), residues: 899 loop : -0.25 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 108 TYR 0.051 0.002 TYR E 643 PHE 0.036 0.003 PHE C 277 TRP 0.033 0.002 TRP B 610 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00510 (24027) covalent geometry : angle 0.77833 (32668) SS BOND : bond 0.00404 ( 43) SS BOND : angle 1.22255 ( 86) hydrogen bonds : bond 0.05207 ( 842) hydrogen bonds : angle 5.76632 ( 2214) link_ALPHA1-2 : bond 0.00645 ( 1) link_ALPHA1-2 : angle 5.35649 ( 3) link_ALPHA1-3 : bond 0.01131 ( 15) link_ALPHA1-3 : angle 2.18584 ( 45) link_ALPHA1-6 : bond 0.00708 ( 16) link_ALPHA1-6 : angle 1.90165 ( 48) link_BETA1-4 : bond 0.01284 ( 29) link_BETA1-4 : angle 3.79835 ( 87) link_NAG-ASN : bond 0.00394 ( 37) link_NAG-ASN : angle 2.52370 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 450 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7036 (tm-30) REVERT: A 112 TRP cc_start: 0.8371 (m100) cc_final: 0.7876 (m100) REVERT: A 180 ASP cc_start: 0.8420 (m-30) cc_final: 0.8061 (m-30) REVERT: A 426 MET cc_start: 0.6069 (mtp) cc_final: 0.5540 (mtp) REVERT: B 530 MET cc_start: 0.2431 (mmp) cc_final: 0.2158 (mmt) REVERT: B 542 ARG cc_start: 0.7756 (ptp90) cc_final: 0.7453 (ptp90) REVERT: B 628 TRP cc_start: 0.3373 (m-10) cc_final: 0.3054 (m-10) REVERT: C 95 MET cc_start: 0.8576 (ptp) cc_final: 0.8362 (ptp) REVERT: C 165 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8088 (mm) REVERT: C 180 ASP cc_start: 0.8674 (m-30) cc_final: 0.8382 (t0) REVERT: C 373 MET cc_start: 0.7489 (mmt) cc_final: 0.7225 (mmm) REVERT: E 644 ASN cc_start: 0.7973 (m-40) cc_final: 0.7726 (t0) REVERT: E 647 GLU cc_start: 0.7569 (pp20) cc_final: 0.7050 (pp20) REVERT: E 648 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8060 (mt-10) REVERT: D 92 ASN cc_start: 0.8454 (t0) cc_final: 0.8178 (t0) REVERT: D 425 ASN cc_start: 0.8115 (p0) cc_final: 0.7794 (p0) REVERT: D 468 PHE cc_start: 0.7930 (m-80) cc_final: 0.7458 (m-80) REVERT: D 486 TYR cc_start: 0.8753 (m-80) cc_final: 0.8544 (m-10) REVERT: F 623 TRP cc_start: 0.8813 (m100) cc_final: 0.8499 (m100) REVERT: F 663 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6854 (tp) REVERT: H 28 THR cc_start: 0.5010 (p) cc_final: 0.4786 (p) REVERT: H 82 MET cc_start: 0.7925 (tpp) cc_final: 0.7223 (tpp) REVERT: L 4 MET cc_start: 0.7097 (mtm) cc_final: 0.6897 (mtm) REVERT: L 27 LEU cc_start: 0.8276 (mt) cc_final: 0.7728 (mt) REVERT: L 42 GLN cc_start: 0.8689 (mp10) cc_final: 0.8145 (mp10) REVERT: L 79 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7427 (tm-30) REVERT: L 94 PHE cc_start: 0.6000 (m-80) cc_final: 0.5773 (m-80) REVERT: L 96 TRP cc_start: 0.7680 (m-90) cc_final: 0.6784 (m-90) REVERT: M 47 TRP cc_start: 0.7942 (t60) cc_final: 0.7289 (t60) REVERT: M 59 TYR cc_start: 0.8551 (m-80) cc_final: 0.8312 (m-80) REVERT: M 72 ASP cc_start: 0.8290 (t0) cc_final: 0.7760 (t0) REVERT: M 86 ASP cc_start: 0.8089 (m-30) cc_final: 0.7824 (m-30) REVERT: M 100 MET cc_start: 0.7132 (ptp) cc_final: 0.6607 (mtt) REVERT: N 24 ASN cc_start: 0.8032 (t0) cc_final: 0.7615 (t0) REVERT: N 25 ASN cc_start: 0.8255 (m-40) cc_final: 0.7986 (m-40) REVERT: N 34 TYR cc_start: 0.8592 (m-80) cc_final: 0.8162 (m-10) REVERT: N 36 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7699 (tm-30) REVERT: N 50 SER cc_start: 0.8192 (p) cc_final: 0.7837 (t) REVERT: N 51 ASP cc_start: 0.6854 (t70) cc_final: 0.6429 (t70) REVERT: N 64 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7905 (ttpp) REVERT: N 70 THR cc_start: 0.8637 (m) cc_final: 0.8329 (p) REVERT: N 87 GLN cc_start: 0.8567 (tt0) cc_final: 0.8201 (tt0) REVERT: N 90 ASP cc_start: 0.8962 (t0) cc_final: 0.8660 (t0) REVERT: N 102 THR cc_start: 0.8653 (p) cc_final: 0.8419 (p) REVERT: O 59 TYR cc_start: 0.6467 (m-80) cc_final: 0.6125 (m-10) REVERT: P 42 GLN cc_start: 0.8876 (mm110) cc_final: 0.8242 (tp40) REVERT: P 51 ILE cc_start: 0.8505 (mm) cc_final: 0.8060 (mp) REVERT: P 71 PHE cc_start: 0.7351 (m-80) cc_final: 0.7071 (m-10) REVERT: P 100 GLN cc_start: 0.7371 (pm20) cc_final: 0.6683 (tm-30) REVERT: Q 36 TRP cc_start: 0.8611 (m100) cc_final: 0.8328 (m100) REVERT: Q 100 MET cc_start: 0.7697 (mmt) cc_final: 0.7056 (mmp) REVERT: R 27 HIS cc_start: 0.7826 (t-90) cc_final: 0.7493 (t-170) REVERT: R 51 ILE cc_start: 0.8374 (mp) cc_final: 0.8155 (mm) REVERT: R 71 PHE cc_start: 0.7384 (m-80) cc_final: 0.6470 (m-80) REVERT: S 58 ASN cc_start: 0.7884 (t0) cc_final: 0.7666 (t0) REVERT: S 72 ASP cc_start: 0.7691 (t0) cc_final: 0.7090 (t0) REVERT: S 75 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8574 (mtmm) outliers start: 99 outliers final: 57 residues processed: 504 average time/residue: 0.1543 time to fit residues: 120.8102 Evaluate side-chains 435 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 225 optimal weight: 30.0000 chunk 258 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 577 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN D 363 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN P 53 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN S 1 GLN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.107788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.083430 restraints weight = 63332.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082943 restraints weight = 47241.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084032 restraints weight = 42347.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084470 restraints weight = 34291.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084622 restraints weight = 31895.650| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24168 Z= 0.193 Angle : 0.784 20.657 33048 Z= 0.382 Chirality : 0.050 0.309 3946 Planarity : 0.005 0.064 4000 Dihedral : 10.164 73.347 5006 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.12 % Rotamer: Outliers : 3.33 % Allowed : 16.06 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2780 helix: 0.59 (0.27), residues: 393 sheet: 0.18 (0.16), residues: 902 loop : -0.37 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 108 TYR 0.029 0.002 TYR E 643 PHE 0.023 0.002 PHE C 277 TRP 0.049 0.002 TRP D 69 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00438 (24027) covalent geometry : angle 0.74216 (32668) SS BOND : bond 0.00386 ( 43) SS BOND : angle 1.29151 ( 86) hydrogen bonds : bond 0.04750 ( 842) hydrogen bonds : angle 5.63575 ( 2214) link_ALPHA1-2 : bond 0.00615 ( 1) link_ALPHA1-2 : angle 5.21925 ( 3) link_ALPHA1-3 : bond 0.01170 ( 15) link_ALPHA1-3 : angle 2.11152 ( 45) link_ALPHA1-6 : bond 0.00704 ( 16) link_ALPHA1-6 : angle 1.90448 ( 48) link_BETA1-4 : bond 0.01161 ( 29) link_BETA1-4 : angle 3.58152 ( 87) link_NAG-ASN : bond 0.00367 ( 37) link_NAG-ASN : angle 2.34746 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 428 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9000 (ppp) cc_final: 0.8698 (ppp) REVERT: A 102 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7046 (tm-30) REVERT: A 180 ASP cc_start: 0.8456 (m-30) cc_final: 0.8093 (m-30) REVERT: B 530 MET cc_start: 0.2521 (mmp) cc_final: 0.2218 (mmt) REVERT: C 165 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7963 (mm) REVERT: C 180 ASP cc_start: 0.8679 (m-30) cc_final: 0.8403 (t0) REVERT: C 373 MET cc_start: 0.7542 (mmt) cc_final: 0.7228 (mmm) REVERT: E 631 TRP cc_start: 0.8783 (t-100) cc_final: 0.8534 (t-100) REVERT: D 92 ASN cc_start: 0.8549 (t0) cc_final: 0.8299 (t0) REVERT: D 373 MET cc_start: 0.6983 (mtp) cc_final: 0.6739 (mmp) REVERT: D 468 PHE cc_start: 0.7885 (m-80) cc_final: 0.7284 (m-80) REVERT: D 486 TYR cc_start: 0.8762 (m-80) cc_final: 0.8499 (m-10) REVERT: F 535 MET cc_start: 0.8303 (tpp) cc_final: 0.8095 (tpt) REVERT: F 623 TRP cc_start: 0.8890 (m100) cc_final: 0.8674 (m100) REVERT: F 663 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (tp) REVERT: H 82 MET cc_start: 0.8022 (tpp) cc_final: 0.7327 (tpp) REVERT: L 4 MET cc_start: 0.6947 (mtm) cc_final: 0.6690 (mtm) REVERT: L 42 GLN cc_start: 0.8662 (mp10) cc_final: 0.8214 (mp10) REVERT: L 93 GLN cc_start: 0.8264 (mm110) cc_final: 0.7926 (mm110) REVERT: L 94 PHE cc_start: 0.6021 (m-80) cc_final: 0.5755 (m-80) REVERT: L 96 TRP cc_start: 0.7782 (m-90) cc_final: 0.7124 (m-90) REVERT: M 72 ASP cc_start: 0.8222 (t0) cc_final: 0.7732 (t0) REVERT: M 86 ASP cc_start: 0.8140 (m-30) cc_final: 0.7772 (m-30) REVERT: M 91 TYR cc_start: 0.7851 (m-80) cc_final: 0.7402 (m-10) REVERT: N 24 ASN cc_start: 0.8110 (t0) cc_final: 0.7687 (t0) REVERT: N 25 ASN cc_start: 0.8227 (m-40) cc_final: 0.8000 (m-40) REVERT: N 34 TYR cc_start: 0.8653 (m-80) cc_final: 0.8241 (m-10) REVERT: N 36 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7900 (tm-30) REVERT: N 50 SER cc_start: 0.8339 (p) cc_final: 0.8043 (t) REVERT: N 51 ASP cc_start: 0.6823 (t70) cc_final: 0.6271 (t70) REVERT: N 70 THR cc_start: 0.8691 (m) cc_final: 0.8405 (p) REVERT: O 100 MET cc_start: 0.7964 (mtp) cc_final: 0.7647 (mmm) REVERT: P 42 GLN cc_start: 0.8906 (mm110) cc_final: 0.8298 (tp40) REVERT: P 51 ILE cc_start: 0.8215 (mm) cc_final: 0.7503 (tp) REVERT: P 71 PHE cc_start: 0.7401 (m-80) cc_final: 0.6904 (m-10) REVERT: Q 12 LEU cc_start: 0.7657 (tp) cc_final: 0.7392 (tp) REVERT: Q 36 TRP cc_start: 0.8595 (m100) cc_final: 0.8272 (m100) REVERT: R 27 HIS cc_start: 0.7977 (t-90) cc_final: 0.7569 (t-170) REVERT: S 58 ASN cc_start: 0.7819 (t0) cc_final: 0.7592 (t0) REVERT: S 72 ASP cc_start: 0.7776 (t0) cc_final: 0.7054 (t0) REVERT: S 75 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8587 (mtmm) REVERT: T 94 ASP cc_start: 0.6774 (t0) cc_final: 0.6549 (t0) outliers start: 83 outliers final: 56 residues processed: 481 average time/residue: 0.1490 time to fit residues: 112.5111 Evaluate side-chains 432 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 374 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 17 GLN Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 99 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN C 195 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 550 GLN H 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN R 37 GLN T 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.104806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077773 restraints weight = 64165.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078582 restraints weight = 40112.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.079474 restraints weight = 29744.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079785 restraints weight = 26079.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079982 restraints weight = 24309.149| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 24168 Z= 0.177 Angle : 0.773 20.635 33048 Z= 0.375 Chirality : 0.049 0.297 3946 Planarity : 0.005 0.048 4000 Dihedral : 9.652 68.922 5006 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 3.65 % Allowed : 16.35 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2780 helix: 0.69 (0.28), residues: 388 sheet: 0.01 (0.16), residues: 952 loop : -0.38 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 542 TYR 0.020 0.002 TYR Q 102 PHE 0.025 0.002 PHE L 71 TRP 0.037 0.002 TRP B 596 HIS 0.010 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00403 (24027) covalent geometry : angle 0.72711 (32668) SS BOND : bond 0.00439 ( 43) SS BOND : angle 2.20952 ( 86) hydrogen bonds : bond 0.04503 ( 842) hydrogen bonds : angle 5.55010 ( 2214) link_ALPHA1-2 : bond 0.00600 ( 1) link_ALPHA1-2 : angle 5.17842 ( 3) link_ALPHA1-3 : bond 0.01175 ( 15) link_ALPHA1-3 : angle 2.05036 ( 45) link_ALPHA1-6 : bond 0.00711 ( 16) link_ALPHA1-6 : angle 1.88029 ( 48) link_BETA1-4 : bond 0.01109 ( 29) link_BETA1-4 : angle 3.47145 ( 87) link_NAG-ASN : bond 0.00356 ( 37) link_NAG-ASN : angle 2.22878 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 402 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9155 (ppp) cc_final: 0.8678 (ppp) REVERT: A 102 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 180 ASP cc_start: 0.8606 (m-30) cc_final: 0.8179 (m-30) REVERT: B 530 MET cc_start: 0.2717 (mmp) cc_final: 0.2434 (mmt) REVERT: B 621 MET cc_start: 0.8195 (ptm) cc_final: 0.7877 (ppp) REVERT: B 628 TRP cc_start: 0.2439 (m-10) cc_final: 0.2227 (m-10) REVERT: C 165 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8082 (mm) REVERT: C 371 ILE cc_start: 0.8892 (mm) cc_final: 0.8609 (tp) REVERT: E 647 GLU cc_start: 0.7630 (pp20) cc_final: 0.7256 (pp20) REVERT: E 648 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8136 (mt-10) REVERT: D 180 ASP cc_start: 0.8092 (m-30) cc_final: 0.7635 (t0) REVERT: D 373 MET cc_start: 0.7260 (mtp) cc_final: 0.6337 (mmt) REVERT: D 468 PHE cc_start: 0.7790 (m-80) cc_final: 0.6972 (m-80) REVERT: D 486 TYR cc_start: 0.8852 (m-80) cc_final: 0.8500 (m-10) REVERT: F 623 TRP cc_start: 0.8975 (m100) cc_final: 0.8304 (m100) REVERT: F 663 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7665 (tp) REVERT: H 82 MET cc_start: 0.7751 (tpp) cc_final: 0.7052 (tpp) REVERT: L 4 MET cc_start: 0.7079 (mtm) cc_final: 0.6663 (mtm) REVERT: L 9 LEU cc_start: 0.8962 (mt) cc_final: 0.8599 (tp) REVERT: L 42 GLN cc_start: 0.8696 (mp10) cc_final: 0.8069 (mp10) REVERT: L 49 TYR cc_start: 0.8164 (p90) cc_final: 0.7698 (p90) REVERT: M 72 ASP cc_start: 0.7945 (t0) cc_final: 0.7221 (t0) REVERT: M 86 ASP cc_start: 0.8149 (m-30) cc_final: 0.7761 (m-30) REVERT: M 91 TYR cc_start: 0.8091 (m-80) cc_final: 0.7406 (m-10) REVERT: N 24 ASN cc_start: 0.8189 (t0) cc_final: 0.7774 (t0) REVERT: N 25 ASN cc_start: 0.8329 (m-40) cc_final: 0.8113 (m-40) REVERT: N 34 TYR cc_start: 0.8576 (m-80) cc_final: 0.8128 (m-10) REVERT: N 36 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7694 (tm-30) REVERT: N 50 SER cc_start: 0.8487 (p) cc_final: 0.8213 (t) REVERT: N 70 THR cc_start: 0.8784 (m) cc_final: 0.8529 (p) REVERT: N 87 GLN cc_start: 0.8214 (tt0) cc_final: 0.8009 (tt0) REVERT: O 100 MET cc_start: 0.8235 (mtp) cc_final: 0.7692 (mmm) REVERT: P 42 GLN cc_start: 0.8773 (mm110) cc_final: 0.8157 (tp40) REVERT: P 51 ILE cc_start: 0.8453 (mm) cc_final: 0.7552 (tp) REVERT: P 71 PHE cc_start: 0.7828 (m-80) cc_final: 0.7370 (m-10) REVERT: Q 13 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8324 (tppt) REVERT: Q 16 GLN cc_start: 0.8157 (mt0) cc_final: 0.7956 (mp10) REVERT: Q 100 MET cc_start: 0.7821 (mmt) cc_final: 0.7406 (mmp) REVERT: R 27 HIS cc_start: 0.8376 (t-90) cc_final: 0.7850 (t70) REVERT: S 58 ASN cc_start: 0.7809 (t0) cc_final: 0.7426 (t0) REVERT: S 72 ASP cc_start: 0.7588 (t0) cc_final: 0.7087 (t0) REVERT: S 75 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8681 (ttpp) REVERT: S 77 GLU cc_start: 0.8103 (tp30) cc_final: 0.7487 (mm-30) outliers start: 91 outliers final: 64 residues processed: 458 average time/residue: 0.1501 time to fit residues: 107.8033 Evaluate side-chains 432 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 274 optimal weight: 5.9990 chunk 165 optimal weight: 0.4980 chunk 275 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN Q 77 HIS ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.106103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.079337 restraints weight = 64406.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.080192 restraints weight = 39098.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.081079 restraints weight = 29226.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082007 restraints weight = 25635.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082015 restraints weight = 23101.657| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24168 Z= 0.138 Angle : 0.723 19.844 33048 Z= 0.349 Chirality : 0.048 0.281 3946 Planarity : 0.004 0.046 4000 Dihedral : 8.945 62.338 5006 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 2.89 % Allowed : 17.39 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2780 helix: 0.84 (0.28), residues: 389 sheet: 0.17 (0.17), residues: 895 loop : -0.45 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 100F TYR 0.019 0.001 TYR N 85 PHE 0.024 0.002 PHE D 317 TRP 0.036 0.002 TRP B 596 HIS 0.007 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (24027) covalent geometry : angle 0.68587 (32668) SS BOND : bond 0.00285 ( 43) SS BOND : angle 1.26327 ( 86) hydrogen bonds : bond 0.04089 ( 842) hydrogen bonds : angle 5.41852 ( 2214) link_ALPHA1-2 : bond 0.00681 ( 1) link_ALPHA1-2 : angle 4.83036 ( 3) link_ALPHA1-3 : bond 0.01208 ( 15) link_ALPHA1-3 : angle 1.96425 ( 45) link_ALPHA1-6 : bond 0.00794 ( 16) link_ALPHA1-6 : angle 1.76479 ( 48) link_BETA1-4 : bond 0.01134 ( 29) link_BETA1-4 : angle 3.26749 ( 87) link_NAG-ASN : bond 0.00374 ( 37) link_NAG-ASN : angle 2.04503 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 405 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9118 (ppp) cc_final: 0.8602 (ppp) REVERT: A 102 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 180 ASP cc_start: 0.8613 (m-30) cc_final: 0.8151 (m-30) REVERT: B 621 MET cc_start: 0.8205 (ptm) cc_final: 0.7824 (ppp) REVERT: C 103 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 165 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8105 (mm) REVERT: C 371 ILE cc_start: 0.8874 (mm) cc_final: 0.8571 (tp) REVERT: E 530 MET cc_start: 0.8865 (mmm) cc_final: 0.8338 (tpp) REVERT: E 647 GLU cc_start: 0.7789 (pp20) cc_final: 0.7420 (pp20) REVERT: E 648 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8116 (mt-10) REVERT: D 66 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (mtm110) REVERT: D 373 MET cc_start: 0.7259 (mtp) cc_final: 0.6418 (mmt) REVERT: D 486 TYR cc_start: 0.8667 (m-80) cc_final: 0.8394 (m-10) REVERT: F 623 TRP cc_start: 0.8948 (m100) cc_final: 0.8144 (m100) REVERT: F 655 LYS cc_start: 0.8029 (tppt) cc_final: 0.7547 (tppt) REVERT: F 663 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7633 (tp) REVERT: H 82 MET cc_start: 0.7643 (tpp) cc_final: 0.6947 (tpp) REVERT: H 100 MET cc_start: 0.7876 (tpp) cc_final: 0.7358 (tpp) REVERT: H 102 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6277 (t80) REVERT: L 4 MET cc_start: 0.7163 (mtm) cc_final: 0.6673 (mtm) REVERT: L 9 LEU cc_start: 0.8968 (mt) cc_final: 0.8618 (tp) REVERT: L 42 GLN cc_start: 0.8691 (mp10) cc_final: 0.8071 (mp10) REVERT: L 46 LEU cc_start: 0.8263 (tt) cc_final: 0.7761 (tt) REVERT: M 56 ASN cc_start: 0.8740 (t0) cc_final: 0.8526 (t0) REVERT: M 72 ASP cc_start: 0.7996 (t0) cc_final: 0.7294 (t0) REVERT: M 86 ASP cc_start: 0.8099 (m-30) cc_final: 0.7642 (m-30) REVERT: M 91 TYR cc_start: 0.8082 (m-80) cc_final: 0.7375 (m-10) REVERT: N 24 ASN cc_start: 0.8350 (t0) cc_final: 0.8056 (p0) REVERT: N 34 TYR cc_start: 0.8565 (m-80) cc_final: 0.8060 (m-10) REVERT: N 36 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7509 (tm-30) REVERT: N 50 SER cc_start: 0.8575 (p) cc_final: 0.8228 (t) REVERT: O 100 MET cc_start: 0.8064 (mtp) cc_final: 0.7581 (mmm) REVERT: P 51 ILE cc_start: 0.8481 (mm) cc_final: 0.7700 (tp) REVERT: P 71 PHE cc_start: 0.7919 (m-80) cc_final: 0.7410 (m-10) REVERT: Q 36 TRP cc_start: 0.8553 (m100) cc_final: 0.7899 (m100) REVERT: Q 100 MET cc_start: 0.7722 (mmt) cc_final: 0.7164 (mmp) REVERT: R 27 HIS cc_start: 0.8298 (t-90) cc_final: 0.7749 (t70) REVERT: R 39 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7012 (mmt90) REVERT: S 4 LEU cc_start: 0.7460 (mp) cc_final: 0.7059 (tt) REVERT: S 58 ASN cc_start: 0.7642 (t0) cc_final: 0.7342 (t0) REVERT: S 72 ASP cc_start: 0.7679 (t0) cc_final: 0.7214 (t0) REVERT: S 75 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8606 (ttpp) REVERT: T 48 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: T 94 ASP cc_start: 0.6819 (t0) cc_final: 0.6274 (t0) outliers start: 72 outliers final: 48 residues processed: 444 average time/residue: 0.1505 time to fit residues: 104.8837 Evaluate side-chains 425 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 123 optimal weight: 0.0470 chunk 131 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 0.0570 chunk 188 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 653 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.105963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078971 restraints weight = 64855.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079690 restraints weight = 41142.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080611 restraints weight = 30594.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.081743 restraints weight = 26744.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081742 restraints weight = 23770.943| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24168 Z= 0.146 Angle : 0.728 20.091 33048 Z= 0.348 Chirality : 0.048 0.284 3946 Planarity : 0.005 0.054 4000 Dihedral : 8.619 59.264 5006 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 3.25 % Allowed : 18.47 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2780 helix: 0.84 (0.28), residues: 388 sheet: 0.15 (0.17), residues: 920 loop : -0.43 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 75 TYR 0.029 0.002 TYR L 49 PHE 0.029 0.002 PHE L 71 TRP 0.039 0.002 TRP B 596 HIS 0.008 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00327 (24027) covalent geometry : angle 0.68906 (32668) SS BOND : bond 0.00430 ( 43) SS BOND : angle 1.72009 ( 86) hydrogen bonds : bond 0.04038 ( 842) hydrogen bonds : angle 5.39227 ( 2214) link_ALPHA1-2 : bond 0.00611 ( 1) link_ALPHA1-2 : angle 4.95924 ( 3) link_ALPHA1-3 : bond 0.01151 ( 15) link_ALPHA1-3 : angle 1.97344 ( 45) link_ALPHA1-6 : bond 0.00751 ( 16) link_ALPHA1-6 : angle 1.78433 ( 48) link_BETA1-4 : bond 0.01191 ( 29) link_BETA1-4 : angle 3.25548 ( 87) link_NAG-ASN : bond 0.00338 ( 37) link_NAG-ASN : angle 2.00780 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 388 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9175 (ppp) cc_final: 0.8654 (ppp) REVERT: A 102 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7553 (tm-30) REVERT: A 180 ASP cc_start: 0.8589 (m-30) cc_final: 0.8118 (m-30) REVERT: B 621 MET cc_start: 0.8211 (ptm) cc_final: 0.7901 (ppp) REVERT: C 92 ASN cc_start: 0.8425 (m-40) cc_final: 0.8076 (p0) REVERT: C 371 ILE cc_start: 0.8881 (mm) cc_final: 0.8586 (tp) REVERT: E 530 MET cc_start: 0.8832 (mmm) cc_final: 0.8316 (tpp) REVERT: E 647 GLU cc_start: 0.7834 (pp20) cc_final: 0.7475 (pp20) REVERT: E 648 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8108 (mt-10) REVERT: D 66 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (mtm110) REVERT: D 125 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8477 (mt) REVERT: D 486 TYR cc_start: 0.8736 (m-80) cc_final: 0.8384 (m-10) REVERT: F 623 TRP cc_start: 0.8981 (m100) cc_final: 0.8219 (m100) REVERT: F 655 LYS cc_start: 0.7916 (tppt) cc_final: 0.7498 (tppt) REVERT: F 663 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7658 (tp) REVERT: H 82 MET cc_start: 0.7685 (tpp) cc_final: 0.7074 (tpp) REVERT: H 100 MET cc_start: 0.7726 (tpp) cc_final: 0.7513 (tpp) REVERT: H 102 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6480 (t80) REVERT: L 4 MET cc_start: 0.7222 (mtm) cc_final: 0.6803 (mtm) REVERT: L 9 LEU cc_start: 0.9025 (mt) cc_final: 0.8627 (tp) REVERT: L 42 GLN cc_start: 0.8695 (mp10) cc_final: 0.8049 (mp10) REVERT: L 46 LEU cc_start: 0.8252 (tt) cc_final: 0.7776 (tt) REVERT: L 71 PHE cc_start: 0.8501 (m-10) cc_final: 0.8209 (m-80) REVERT: L 77 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8509 (ptp-170) REVERT: L 94 PHE cc_start: 0.5059 (m-80) cc_final: 0.4564 (m-80) REVERT: M 13 LYS cc_start: 0.9256 (tppt) cc_final: 0.9027 (mmmt) REVERT: M 46 GLU cc_start: 0.8370 (tp30) cc_final: 0.8127 (tp30) REVERT: M 47 TRP cc_start: 0.6237 (t60) cc_final: 0.5920 (t60) REVERT: M 58 ASN cc_start: 0.7825 (t0) cc_final: 0.7274 (t0) REVERT: M 72 ASP cc_start: 0.8004 (t0) cc_final: 0.7285 (t0) REVERT: M 86 ASP cc_start: 0.8135 (m-30) cc_final: 0.7641 (m-30) REVERT: M 91 TYR cc_start: 0.8185 (m-80) cc_final: 0.7447 (m-10) REVERT: N 34 TYR cc_start: 0.8637 (m-80) cc_final: 0.8131 (m-10) REVERT: N 36 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7556 (tm-30) REVERT: N 50 SER cc_start: 0.8581 (p) cc_final: 0.8211 (t) REVERT: O 100 MET cc_start: 0.7904 (mtp) cc_final: 0.7490 (mmm) REVERT: P 42 GLN cc_start: 0.8674 (mm110) cc_final: 0.7912 (tm-30) REVERT: P 51 ILE cc_start: 0.8522 (mm) cc_final: 0.7737 (tp) REVERT: P 71 PHE cc_start: 0.7915 (m-80) cc_final: 0.7457 (m-10) REVERT: Q 57 THR cc_start: 0.9138 (p) cc_final: 0.8893 (t) REVERT: Q 100 MET cc_start: 0.7696 (mmt) cc_final: 0.7198 (mmp) REVERT: R 27 HIS cc_start: 0.8313 (t-90) cc_final: 0.7732 (t70) REVERT: R 42 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7231 (mm-40) REVERT: S 4 LEU cc_start: 0.7608 (mp) cc_final: 0.7211 (tt) REVERT: S 58 ASN cc_start: 0.7665 (t0) cc_final: 0.7364 (t0) REVERT: S 72 ASP cc_start: 0.7576 (t0) cc_final: 0.7078 (t0) REVERT: S 75 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8560 (ttpp) REVERT: S 100 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6710 (mm-30) REVERT: T 48 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: T 73 ILE cc_start: 0.8888 (mp) cc_final: 0.8519 (mt) REVERT: T 94 ASP cc_start: 0.6924 (t0) cc_final: 0.6518 (t0) outliers start: 81 outliers final: 54 residues processed: 435 average time/residue: 0.1489 time to fit residues: 101.8593 Evaluate side-chains 421 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 170 GLN E 591 GLN E 616 ASN D 203 GLN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077472 restraints weight = 63635.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078921 restraints weight = 39610.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079585 restraints weight = 28321.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080600 restraints weight = 26131.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.080687 restraints weight = 23130.266| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24168 Z= 0.165 Angle : 0.727 20.051 33048 Z= 0.349 Chirality : 0.048 0.287 3946 Planarity : 0.005 0.046 4000 Dihedral : 8.247 58.054 5006 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.37 % Allowed : 18.31 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2780 helix: 0.83 (0.28), residues: 388 sheet: 0.23 (0.17), residues: 905 loop : -0.55 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 100F TYR 0.027 0.002 TYR N 85 PHE 0.034 0.002 PHE A 93 TRP 0.046 0.002 TRP B 596 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00374 (24027) covalent geometry : angle 0.69109 (32668) SS BOND : bond 0.00319 ( 43) SS BOND : angle 0.97618 ( 86) hydrogen bonds : bond 0.04069 ( 842) hydrogen bonds : angle 5.38267 ( 2214) link_ALPHA1-2 : bond 0.00551 ( 1) link_ALPHA1-2 : angle 4.98081 ( 3) link_ALPHA1-3 : bond 0.01107 ( 15) link_ALPHA1-3 : angle 2.00521 ( 45) link_ALPHA1-6 : bond 0.00689 ( 16) link_ALPHA1-6 : angle 1.81436 ( 48) link_BETA1-4 : bond 0.01154 ( 29) link_BETA1-4 : angle 3.25613 ( 87) link_NAG-ASN : bond 0.00335 ( 37) link_NAG-ASN : angle 2.01391 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 378 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9216 (ppp) cc_final: 0.8680 (ppp) REVERT: A 102 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 180 ASP cc_start: 0.8624 (m-30) cc_final: 0.8181 (m-30) REVERT: A 475 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7357 (ptp) REVERT: C 92 ASN cc_start: 0.8448 (m-40) cc_final: 0.8090 (p0) REVERT: C 103 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 371 ILE cc_start: 0.8923 (mm) cc_final: 0.8617 (tp) REVERT: E 530 MET cc_start: 0.8807 (mmm) cc_final: 0.8330 (tpp) REVERT: E 621 MET cc_start: 0.8112 (ppp) cc_final: 0.7854 (ppp) REVERT: E 647 GLU cc_start: 0.7850 (pp20) cc_final: 0.7485 (pp20) REVERT: E 648 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8102 (mt-10) REVERT: D 125 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 373 MET cc_start: 0.7088 (mtp) cc_final: 0.6721 (mmt) REVERT: D 486 TYR cc_start: 0.8768 (m-80) cc_final: 0.8437 (m-10) REVERT: F 623 TRP cc_start: 0.9015 (m100) cc_final: 0.8277 (m100) REVERT: F 663 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7580 (tp) REVERT: H 82 MET cc_start: 0.7734 (tpp) cc_final: 0.7112 (tpp) REVERT: H 102 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6647 (t80) REVERT: L 4 MET cc_start: 0.7364 (mtm) cc_final: 0.6922 (mtm) REVERT: L 9 LEU cc_start: 0.9044 (mt) cc_final: 0.8645 (tp) REVERT: L 42 GLN cc_start: 0.8754 (mp10) cc_final: 0.8084 (mp10) REVERT: L 46 LEU cc_start: 0.8247 (tt) cc_final: 0.7829 (tt) REVERT: L 71 PHE cc_start: 0.8591 (m-10) cc_final: 0.8239 (m-80) REVERT: L 77 ARG cc_start: 0.8822 (mtm110) cc_final: 0.8474 (ptp-170) REVERT: L 94 PHE cc_start: 0.5114 (m-80) cc_final: 0.4635 (m-80) REVERT: M 46 GLU cc_start: 0.8353 (tp30) cc_final: 0.8070 (tp30) REVERT: M 47 TRP cc_start: 0.6224 (t60) cc_final: 0.5869 (t60) REVERT: M 58 ASN cc_start: 0.7873 (t0) cc_final: 0.6954 (t0) REVERT: M 72 ASP cc_start: 0.7955 (t0) cc_final: 0.7268 (t0) REVERT: M 86 ASP cc_start: 0.8092 (m-30) cc_final: 0.7605 (m-30) REVERT: M 91 TYR cc_start: 0.8164 (m-80) cc_final: 0.7342 (m-10) REVERT: N 34 TYR cc_start: 0.8600 (m-80) cc_final: 0.8098 (m-10) REVERT: N 36 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7513 (tm-30) REVERT: N 50 SER cc_start: 0.8662 (p) cc_final: 0.8293 (t) REVERT: N 94 ASP cc_start: 0.7446 (t0) cc_final: 0.6728 (t0) REVERT: O 100 MET cc_start: 0.7923 (mtp) cc_final: 0.7468 (mmm) REVERT: P 42 GLN cc_start: 0.8685 (mm110) cc_final: 0.8013 (tm-30) REVERT: P 51 ILE cc_start: 0.8566 (mm) cc_final: 0.7748 (tp) REVERT: P 71 PHE cc_start: 0.7960 (m-80) cc_final: 0.7560 (m-10) REVERT: Q 57 THR cc_start: 0.9227 (p) cc_final: 0.8983 (t) REVERT: Q 100 MET cc_start: 0.7678 (mmt) cc_final: 0.7223 (mmp) REVERT: R 27 HIS cc_start: 0.8327 (t-90) cc_final: 0.7686 (t70) REVERT: S 4 LEU cc_start: 0.7533 (mp) cc_final: 0.7266 (tt) REVERT: S 58 ASN cc_start: 0.7741 (t0) cc_final: 0.7337 (t0) REVERT: S 72 ASP cc_start: 0.7628 (t0) cc_final: 0.7129 (t0) REVERT: S 75 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8615 (ttpp) REVERT: S 100 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6708 (mm-30) REVERT: S 105 GLN cc_start: 0.8285 (mp10) cc_final: 0.7886 (tp40) REVERT: T 33 TRP cc_start: 0.7044 (m100) cc_final: 0.6842 (m100) REVERT: T 48 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: T 71 LEU cc_start: 0.8473 (tp) cc_final: 0.8196 (tp) REVERT: T 73 ILE cc_start: 0.8827 (mp) cc_final: 0.8515 (mt) outliers start: 84 outliers final: 61 residues processed: 430 average time/residue: 0.1425 time to fit residues: 97.1130 Evaluate side-chains 425 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 359 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 100 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 139 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 616 ASN D 246 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN P 38 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.106480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080166 restraints weight = 67484.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080565 restraints weight = 45767.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081325 restraints weight = 36402.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081583 restraints weight = 31300.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081811 restraints weight = 29492.423| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24168 Z= 0.209 Angle : 0.766 20.433 33048 Z= 0.368 Chirality : 0.049 0.295 3946 Planarity : 0.005 0.048 4000 Dihedral : 8.024 59.740 5006 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 3.29 % Allowed : 18.88 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2780 helix: 0.75 (0.28), residues: 388 sheet: 0.19 (0.17), residues: 904 loop : -0.56 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 75 TYR 0.032 0.002 TYR L 49 PHE 0.031 0.003 PHE S 78 TRP 0.054 0.002 TRP B 596 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00481 (24027) covalent geometry : angle 0.72940 (32668) SS BOND : bond 0.00505 ( 43) SS BOND : angle 1.06659 ( 86) hydrogen bonds : bond 0.04291 ( 842) hydrogen bonds : angle 5.48152 ( 2214) link_ALPHA1-2 : bond 0.00475 ( 1) link_ALPHA1-2 : angle 4.94528 ( 3) link_ALPHA1-3 : bond 0.01067 ( 15) link_ALPHA1-3 : angle 2.06751 ( 45) link_ALPHA1-6 : bond 0.00612 ( 16) link_ALPHA1-6 : angle 1.91263 ( 48) link_BETA1-4 : bond 0.01100 ( 29) link_BETA1-4 : angle 3.34248 ( 87) link_NAG-ASN : bond 0.00333 ( 37) link_NAG-ASN : angle 2.09144 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 363 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9202 (ppp) cc_final: 0.8981 (ppp) REVERT: A 102 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 104 MET cc_start: 0.8740 (tpp) cc_final: 0.7775 (tpp) REVERT: A 180 ASP cc_start: 0.8614 (m-30) cc_final: 0.8136 (m-30) REVERT: B 628 TRP cc_start: 0.2931 (m-10) cc_final: 0.2668 (m-10) REVERT: C 92 ASN cc_start: 0.8436 (m-40) cc_final: 0.8105 (p0) REVERT: C 103 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 371 ILE cc_start: 0.8999 (mm) cc_final: 0.8711 (tp) REVERT: E 530 MET cc_start: 0.8703 (mmm) cc_final: 0.8222 (tpp) REVERT: E 647 GLU cc_start: 0.7782 (pp20) cc_final: 0.7442 (pp20) REVERT: E 648 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8133 (mt-10) REVERT: D 125 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8534 (mt) REVERT: D 373 MET cc_start: 0.7215 (mtp) cc_final: 0.6833 (mmt) REVERT: D 486 TYR cc_start: 0.8861 (m-80) cc_final: 0.8578 (m-10) REVERT: F 623 TRP cc_start: 0.9083 (m100) cc_final: 0.8808 (m100) REVERT: F 663 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7989 (tp) REVERT: H 82 MET cc_start: 0.7860 (tpp) cc_final: 0.7202 (tpp) REVERT: H 102 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6990 (t80) REVERT: L 4 MET cc_start: 0.7434 (mtm) cc_final: 0.7004 (mtm) REVERT: L 9 LEU cc_start: 0.8998 (mt) cc_final: 0.8612 (tp) REVERT: L 42 GLN cc_start: 0.8706 (mp10) cc_final: 0.8087 (mp10) REVERT: L 77 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8443 (ptp-170) REVERT: M 46 GLU cc_start: 0.8453 (tp30) cc_final: 0.8138 (tp30) REVERT: M 47 TRP cc_start: 0.6646 (t60) cc_final: 0.6243 (t60) REVERT: M 58 ASN cc_start: 0.8015 (t0) cc_final: 0.7072 (t0) REVERT: M 72 ASP cc_start: 0.8013 (t0) cc_final: 0.7330 (t0) REVERT: M 86 ASP cc_start: 0.8217 (m-30) cc_final: 0.7723 (m-30) REVERT: N 34 TYR cc_start: 0.8732 (m-80) cc_final: 0.8276 (m-10) REVERT: N 36 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7613 (tm-30) REVERT: N 50 SER cc_start: 0.8660 (p) cc_final: 0.8328 (t) REVERT: N 94 ASP cc_start: 0.7635 (t0) cc_final: 0.6868 (t0) REVERT: O 100 MET cc_start: 0.7818 (mtp) cc_final: 0.7429 (mmm) REVERT: P 42 GLN cc_start: 0.8750 (mm110) cc_final: 0.8041 (tm-30) REVERT: P 71 PHE cc_start: 0.7941 (m-80) cc_final: 0.7584 (m-10) REVERT: Q 100 MET cc_start: 0.7656 (mmt) cc_final: 0.7175 (mmp) REVERT: R 27 HIS cc_start: 0.8268 (t-90) cc_final: 0.7574 (t-170) REVERT: R 42 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7239 (mm-40) REVERT: S 29 ILE cc_start: 0.8889 (mm) cc_final: 0.8683 (mm) REVERT: S 58 ASN cc_start: 0.7961 (t0) cc_final: 0.7687 (t0) REVERT: S 72 ASP cc_start: 0.7557 (t0) cc_final: 0.7106 (t0) REVERT: S 75 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8683 (ttpp) REVERT: S 100 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7510 (mt-10) REVERT: S 105 GLN cc_start: 0.8317 (mp10) cc_final: 0.8007 (tp40) REVERT: T 33 TRP cc_start: 0.7316 (m100) cc_final: 0.6904 (m100) REVERT: T 48 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.6576 (m-80) REVERT: T 73 ILE cc_start: 0.8923 (mp) cc_final: 0.8442 (mt) outliers start: 82 outliers final: 65 residues processed: 412 average time/residue: 0.1486 time to fit residues: 96.9190 Evaluate side-chains 420 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 351 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 178 optimal weight: 0.0470 chunk 257 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS B 551 GLN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.103317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.076556 restraints weight = 63857.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077343 restraints weight = 39639.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078161 restraints weight = 29574.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078555 restraints weight = 25859.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078694 restraints weight = 24078.221| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24168 Z= 0.197 Angle : 0.781 20.425 33048 Z= 0.374 Chirality : 0.049 0.328 3946 Planarity : 0.005 0.063 4000 Dihedral : 7.989 59.338 5006 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.00 % Favored : 94.93 % Rotamer: Outliers : 2.93 % Allowed : 19.24 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2780 helix: 0.67 (0.29), residues: 388 sheet: 0.14 (0.17), residues: 885 loop : -0.56 (0.17), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG T 75 TYR 0.042 0.002 TYR L 49 PHE 0.033 0.003 PHE S 53 TRP 0.074 0.002 TRP A 427 HIS 0.007 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00454 (24027) covalent geometry : angle 0.74265 (32668) SS BOND : bond 0.00372 ( 43) SS BOND : angle 1.69368 ( 86) hydrogen bonds : bond 0.04307 ( 842) hydrogen bonds : angle 5.50347 ( 2214) link_ALPHA1-2 : bond 0.00540 ( 1) link_ALPHA1-2 : angle 5.09214 ( 3) link_ALPHA1-3 : bond 0.01060 ( 15) link_ALPHA1-3 : angle 2.04971 ( 45) link_ALPHA1-6 : bond 0.00605 ( 16) link_ALPHA1-6 : angle 1.87163 ( 48) link_BETA1-4 : bond 0.01076 ( 29) link_BETA1-4 : angle 3.34860 ( 87) link_NAG-ASN : bond 0.00315 ( 37) link_NAG-ASN : angle 2.07007 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 369 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 104 MET cc_start: 0.8773 (tpp) cc_final: 0.7798 (tpp) REVERT: A 107 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8481 (t0) REVERT: A 110 SER cc_start: 0.9411 (m) cc_final: 0.9002 (p) REVERT: A 180 ASP cc_start: 0.8630 (m-30) cc_final: 0.8091 (m-30) REVERT: A 425 ASN cc_start: 0.8464 (m-40) cc_final: 0.8224 (m-40) REVERT: B 621 MET cc_start: 0.7816 (ppp) cc_final: 0.7607 (ppp) REVERT: B 628 TRP cc_start: 0.3265 (m-10) cc_final: 0.3002 (m-10) REVERT: C 92 ASN cc_start: 0.8439 (m-40) cc_final: 0.8075 (p0) REVERT: C 103 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 371 ILE cc_start: 0.9031 (mm) cc_final: 0.8746 (tp) REVERT: E 530 MET cc_start: 0.8695 (mmm) cc_final: 0.8176 (tpp) REVERT: E 584 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: E 647 GLU cc_start: 0.7778 (pp20) cc_final: 0.7432 (pp20) REVERT: E 648 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8155 (mt-10) REVERT: D 125 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8714 (mt) REVERT: D 373 MET cc_start: 0.7253 (mtp) cc_final: 0.6810 (mmt) REVERT: D 427 TRP cc_start: 0.7870 (m100) cc_final: 0.7196 (m100) REVERT: D 486 TYR cc_start: 0.8864 (m-80) cc_final: 0.8574 (m-10) REVERT: F 535 MET cc_start: 0.9126 (tpp) cc_final: 0.8924 (tpt) REVERT: F 621 MET cc_start: 0.8530 (tpp) cc_final: 0.8156 (tpp) REVERT: F 623 TRP cc_start: 0.9106 (m100) cc_final: 0.8849 (m100) REVERT: H 82 MET cc_start: 0.7758 (tpp) cc_final: 0.7113 (tpp) REVERT: H 102 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6949 (t80) REVERT: L 4 MET cc_start: 0.7502 (mtm) cc_final: 0.6914 (mtm) REVERT: L 9 LEU cc_start: 0.9018 (mt) cc_final: 0.8628 (tp) REVERT: L 42 GLN cc_start: 0.8663 (mp10) cc_final: 0.8002 (mp10) REVERT: L 77 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8461 (ptp-170) REVERT: M 46 GLU cc_start: 0.8432 (tp30) cc_final: 0.8089 (tp30) REVERT: M 47 TRP cc_start: 0.6589 (t60) cc_final: 0.6200 (t60) REVERT: M 58 ASN cc_start: 0.7924 (t0) cc_final: 0.7013 (t0) REVERT: M 72 ASP cc_start: 0.8032 (t0) cc_final: 0.7278 (t0) REVERT: M 86 ASP cc_start: 0.8165 (m-30) cc_final: 0.7647 (m-30) REVERT: N 34 TYR cc_start: 0.8635 (m-80) cc_final: 0.8173 (m-10) REVERT: N 36 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7586 (tm-30) REVERT: N 50 SER cc_start: 0.8755 (p) cc_final: 0.8384 (t) REVERT: N 94 ASP cc_start: 0.7486 (t0) cc_final: 0.6770 (t0) REVERT: O 100 MET cc_start: 0.7890 (mtp) cc_final: 0.7473 (mmm) REVERT: P 42 GLN cc_start: 0.8751 (mm110) cc_final: 0.8051 (tm-30) REVERT: P 71 PHE cc_start: 0.8019 (m-80) cc_final: 0.7591 (m-10) REVERT: Q 72 ASP cc_start: 0.7734 (t0) cc_final: 0.7330 (t70) REVERT: Q 100 MET cc_start: 0.7631 (mmt) cc_final: 0.7202 (mmp) REVERT: R 27 HIS cc_start: 0.8315 (t-90) cc_final: 0.7599 (t-170) REVERT: R 42 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7240 (mm-40) REVERT: S 29 ILE cc_start: 0.8932 (mm) cc_final: 0.8722 (mm) REVERT: S 58 ASN cc_start: 0.7872 (t0) cc_final: 0.7576 (t0) REVERT: S 72 ASP cc_start: 0.7615 (t0) cc_final: 0.7106 (t0) REVERT: S 75 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8656 (ttpp) REVERT: S 100 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6769 (mm-30) REVERT: S 105 GLN cc_start: 0.8246 (mp10) cc_final: 0.7923 (tp40) REVERT: T 33 TRP cc_start: 0.7433 (m100) cc_final: 0.6922 (m100) REVERT: T 48 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6635 (m-80) outliers start: 73 outliers final: 63 residues processed: 412 average time/residue: 0.1505 time to fit residues: 97.8014 Evaluate side-chains 419 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 351 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 100 TRP Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 45 VAL Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 222 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 chunk 213 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.0570 chunk 98 optimal weight: 0.0970 chunk 254 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN M 100CASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.108943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081939 restraints weight = 65084.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.083455 restraints weight = 38762.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084121 restraints weight = 28897.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084452 restraints weight = 25623.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084551 restraints weight = 24010.923| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24168 Z= 0.128 Angle : 0.731 20.139 33048 Z= 0.347 Chirality : 0.048 0.274 3946 Planarity : 0.004 0.048 4000 Dihedral : 7.443 59.931 5006 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 2.21 % Allowed : 19.96 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 2780 helix: 0.78 (0.29), residues: 388 sheet: 0.28 (0.17), residues: 884 loop : -0.58 (0.17), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 75 TYR 0.034 0.001 TYR L 49 PHE 0.033 0.002 PHE S 53 TRP 0.055 0.002 TRP B 596 HIS 0.008 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (24027) covalent geometry : angle 0.69717 (32668) SS BOND : bond 0.00240 ( 43) SS BOND : angle 1.44565 ( 86) hydrogen bonds : bond 0.03769 ( 842) hydrogen bonds : angle 5.34371 ( 2214) link_ALPHA1-2 : bond 0.00585 ( 1) link_ALPHA1-2 : angle 4.69126 ( 3) link_ALPHA1-3 : bond 0.01129 ( 15) link_ALPHA1-3 : angle 1.88013 ( 45) link_ALPHA1-6 : bond 0.00748 ( 16) link_ALPHA1-6 : angle 1.57363 ( 48) link_BETA1-4 : bond 0.01118 ( 29) link_BETA1-4 : angle 3.18851 ( 87) link_NAG-ASN : bond 0.00394 ( 37) link_NAG-ASN : angle 1.85288 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.03 seconds wall clock time: 66 minutes 9.23 seconds (3969.23 seconds total)