Starting phenix.real_space_refine on Wed Mar 4 20:30:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8e_23231/03_2026/7l8e_23231.cif" } resolution = 4.2 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= 0.000 sd= 0.003 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 102 5.16 5 C 9840 2.51 5 N 2662 2.21 5 O 3223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 15827 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3486 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1003 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "A" Number of atoms: 3514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3514 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 968 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "G" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 3.61, per 1000 atoms: 0.23 Number of scatterers: 15827 At special positions: 0 Unit cell: (133.9, 127.72, 142.14, 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 102 16.00 O 3223 8.00 N 2662 7.00 C 9840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.09 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 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=2.08 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=2.09 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 D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA X 3 " - " MAN X 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 295 " " NAG A 704 " - " ASN A 386 " " NAG A 705 " - " ASN A 363 " " NAG A 706 " - " ASN A 234 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 241 " " NAG A 709 " - " ASN A 289 " " NAG A 710 " - " ASN A 339 " " NAG A 711 " - " ASN A 355 " " NAG A 712 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 276 " " NAG C 703 " - " ASN C 386 " " NAG C 704 " - " ASN C 363 " " NAG C 705 " - " ASN C 133 " " NAG C 706 " - " ASN C 88 " " NAG C 707 " - " ASN C 241 " " NAG C 708 " - " ASN C 289 " " NAG C 709 " - " ASN C 339 " " NAG C 710 " - " ASN C 355 " " NAG C 711 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 701 " - " ASN E 160 " " NAG E 702 " - " ASN E 276 " " NAG E 703 " - " ASN E 386 " " NAG E 704 " - " ASN E 363 " " NAG E 705 " - " ASN E 234 " " NAG E 706 " - " ASN E 133 " " NAG E 707 " - " ASN E 301 " " NAG E 708 " - " ASN E 88 " " NAG E 709 " - " ASN E 289 " " NAG E 710 " - " ASN E 339 " " NAG E 711 " - " ASN E 355 " " NAG E 712 " - " ASN E 392 " " NAG E 713 " - " ASN E 137 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 448 " " NAG S 1 " - " ASN E 295 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 241 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN A 262 " " NAG Y 1 " - " ASN A 448 " " NAG Z 1 " - " ASN A 197 " " NAG a 1 " - " ASN A 301 " " NAG b 1 " - " ASN A 88 " " NAG c 1 " - " ASN A 332 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 575.3 milliseconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 49 sheets defined 29.6% alpha, 71.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.630A 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 139 through 151 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.790A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.319A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.726A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 634 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.025A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.817A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.197A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.090A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.967A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.591A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 634 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'L' and resid 25 through 31 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.117A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.864A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.762A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.604A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.738A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.851A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.828A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.791A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.270A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.214A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 323 through 323A removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.013A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 10.903A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.491A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.590A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.561A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.427A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AE4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AE5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AE6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.544A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.623A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.641A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.675A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.543A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 301 through 312 removed outlier: 7.130A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 49 through 50 Processing sheet with id=AF2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.006A pdb=" N UNK L 84 " --> pdb=" O UNK L 99 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N UNK L 99 " --> pdb=" O UNK L 84 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2202 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: 3.04 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3760 1.32 - 1.46: 4949 1.46 - 1.60: 7232 1.60 - 1.74: 25 1.74 - 1.88: 132 Bond restraints: 16098 Sorted by residual: bond pdb=" CB TYR C 319 " pdb=" CG TYR C 319 " ideal model delta sigma weight residual 1.512 1.348 0.164 2.20e-02 2.07e+03 5.59e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.21e+01 bond pdb=" CB TYR E 484 " pdb=" CG TYR E 484 " ideal model delta sigma weight residual 1.512 1.371 0.141 2.20e-02 2.07e+03 4.11e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.03e+01 bond pdb=" NE1 TRP D 628 " pdb=" CE2 TRP D 628 " ideal model delta sigma weight residual 1.370 1.311 0.059 1.10e-02 8.26e+03 2.89e+01 ... (remaining 16093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 20261 3.13 - 6.26: 1529 6.26 - 9.40: 98 9.40 - 12.53: 5 12.53 - 15.66: 1 Bond angle restraints: 21894 Sorted by residual: angle pdb=" C VAL C 75 " pdb=" N PRO C 76 " pdb=" CA PRO C 76 " ideal model delta sigma weight residual 119.56 128.63 -9.07 1.02e+00 9.61e-01 7.91e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.61 -9.05 1.02e+00 9.61e-01 7.86e+01 angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.47 101.99 8.48 9.60e-01 1.09e+00 7.80e+01 angle pdb=" C GLY A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta sigma weight residual 119.78 128.60 -8.82 1.03e+00 9.43e-01 7.34e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.19 -8.63 1.02e+00 9.61e-01 7.16e+01 ... (remaining 21889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10551 21.23 - 42.47: 230 42.47 - 63.70: 76 63.70 - 84.93: 27 84.93 - 106.17: 19 Dihedral angle restraints: 10903 sinusoidal: 5362 harmonic: 5541 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.82 45.82 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -110.19 -12.41 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -126.96 40.96 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 10900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1779 0.101 - 0.202: 613 0.202 - 0.303: 226 0.303 - 0.404: 106 0.404 - 0.505: 69 Chirality restraints: 2793 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.46e+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 -2.16 -0.24 2.00e-02 2.50e+03 1.43e+02 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 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 ... (remaining 2790 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Z 2 " -0.344 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG Z 2 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG Z 2 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG Z 2 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG Z 2 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.341 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.333 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG B 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.083 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3198 2.78 - 3.31: 15129 3.31 - 3.84: 25697 3.84 - 4.37: 31272 4.37 - 4.90: 48739 Nonbonded interactions: 124035 Sorted by model distance: nonbonded pdb=" O3 NAG X 1 " pdb=" O7 NAG X 1 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 325 " pdb=" OD1 ASP A 325 " model vdw 2.362 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.376 3.040 nonbonded pdb=" N TYR D 638 " pdb=" N THR D 639 " model vdw 2.386 2.560 nonbonded pdb=" NZ LYS E 46 " pdb=" OD2 ASP F 632 " model vdw 2.396 3.120 ... (remaining 124030 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' and (resid 33 through 56 or resid 66 through 397 or resid 411 through \ 505 or resid 702 through 712)) selection = (chain 'C' and (resid 33 through 56 or resid 66 through 505 or resid 701 through \ 711)) selection = (chain 'E' and (resid 33 through 56 or resid 66 through 505 or resid 702 through \ 712)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = (chain 'D' and (resid 520 through 546 or resid 568 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 520 through 546 or resid 568 through 661 or resid 702 thro \ ugh 703)) } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = (chain 'H' and resid 14 through 112) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 3.080 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.470 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.023 0.164 16226 Z= 1.206 Angle : 1.768 15.659 22245 Z= 1.118 Chirality : 0.145 0.505 2793 Planarity : 0.018 0.295 2680 Dihedral : 11.274 106.167 7200 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.06 % 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: 1.11 (0.19), residues: 1666 helix: 0.42 (0.23), residues: 418 sheet: 1.17 (0.24), residues: 402 loop : 0.87 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 327 TYR 0.052 0.009 TYR C 40 PHE 0.035 0.006 PHE C 233 TRP 0.070 0.010 TRP E 35 HIS 0.011 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02203 (16098) covalent geometry : angle 1.73873 (21894) SS BOND : bond 0.01971 ( 33) SS BOND : angle 2.91255 ( 66) hydrogen bonds : bond 0.16830 ( 591) hydrogen bonds : angle 7.85416 ( 2202) link_ALPHA1-3 : bond 0.07060 ( 3) link_ALPHA1-3 : angle 3.78367 ( 9) link_ALPHA1-6 : bond 0.04692 ( 3) link_ALPHA1-6 : angle 2.75848 ( 9) link_BETA1-4 : bond 0.07056 ( 24) link_BETA1-4 : angle 4.30042 ( 72) link_NAG-ASN : bond 0.07413 ( 65) link_NAG-ASN : angle 2.56469 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.527 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: C 125 LEU cc_start: 0.9469 (mt) cc_final: 0.9232 (mt) REVERT: C 195 ASN cc_start: 0.8890 (p0) cc_final: 0.8688 (p0) REVERT: C 338 TRP cc_start: 0.9142 (t-100) cc_final: 0.8681 (t-100) REVERT: C 390 LEU cc_start: 0.9577 (mt) cc_final: 0.8959 (mt) REVERT: C 486 TYR cc_start: 0.8927 (m-80) cc_final: 0.8395 (m-80) REVERT: D 574 LYS cc_start: 0.9264 (mttt) cc_final: 0.8960 (mttp) REVERT: D 634 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8579 (mm-30) REVERT: D 639 THR cc_start: 0.9074 (m) cc_final: 0.8122 (p) REVERT: D 645 LEU cc_start: 0.9087 (mt) cc_final: 0.8151 (mt) REVERT: D 663 LEU cc_start: 0.7999 (tp) cc_final: 0.7724 (tt) REVERT: E 103 GLN cc_start: 0.8707 (tt0) cc_final: 0.8299 (tp40) REVERT: E 107 ASP cc_start: 0.9068 (m-30) cc_final: 0.8845 (m-30) REVERT: E 180 ASP cc_start: 0.9157 (m-30) cc_final: 0.8723 (m-30) REVERT: E 390 LEU cc_start: 0.9637 (mt) cc_final: 0.9206 (mt) REVERT: E 426 MET cc_start: 0.8489 (mtp) cc_final: 0.8232 (mtp) REVERT: E 434 MET cc_start: 0.9490 (ttp) cc_final: 0.9258 (ttp) REVERT: F 543 ASN cc_start: 0.8449 (m-40) cc_final: 0.8140 (m110) REVERT: F 571 TRP cc_start: 0.8890 (t60) cc_final: 0.8686 (t60) REVERT: F 577 GLN cc_start: 0.9069 (mt0) cc_final: 0.8775 (mt0) REVERT: F 639 THR cc_start: 0.8258 (m) cc_final: 0.6267 (p) REVERT: A 180 ASP cc_start: 0.8591 (m-30) cc_final: 0.8353 (m-30) REVERT: A 284 ILE cc_start: 0.9606 (mt) cc_final: 0.9328 (pt) REVERT: A 430 ILE cc_start: 0.8933 (mm) cc_final: 0.8715 (tp) REVERT: B 545 LEU cc_start: 0.8793 (mt) cc_final: 0.8195 (mm) REVERT: B 586 TYR cc_start: 0.9318 (t80) cc_final: 0.8730 (t80) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.1245 time to fit residues: 85.4268 Evaluate side-chains 233 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 585 HIS F 651 ASN A 103 GLN A 137 ASN A 195 ASN A 328 GLN A 425 ASN A 462 ASN B 540 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.061883 restraints weight = 65378.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063368 restraints weight = 40288.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064406 restraints weight = 29404.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065037 restraints weight = 23778.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.065532 restraints weight = 20774.267| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16226 Z= 0.217 Angle : 0.876 17.930 22245 Z= 0.425 Chirality : 0.051 0.284 2793 Planarity : 0.005 0.066 2680 Dihedral : 9.419 81.203 3986 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.33 % Allowed : 2.56 % Favored : 97.11 % 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: 0.78 (0.19), residues: 1666 helix: 1.37 (0.25), residues: 410 sheet: 0.78 (0.24), residues: 421 loop : 0.04 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 542 TYR 0.028 0.003 TYR C 217 PHE 0.027 0.003 PHE C 383 TRP 0.034 0.002 TRP D 631 HIS 0.010 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00473 (16098) covalent geometry : angle 0.81010 (21894) SS BOND : bond 0.00532 ( 33) SS BOND : angle 1.18998 ( 66) hydrogen bonds : bond 0.06436 ( 591) hydrogen bonds : angle 5.29161 ( 2202) link_ALPHA1-3 : bond 0.01157 ( 3) link_ALPHA1-3 : angle 2.43995 ( 9) link_ALPHA1-6 : bond 0.00724 ( 3) link_ALPHA1-6 : angle 1.87786 ( 9) link_BETA1-4 : bond 0.00639 ( 24) link_BETA1-4 : angle 2.38822 ( 72) link_NAG-ASN : bond 0.00657 ( 65) link_NAG-ASN : angle 3.29487 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.545 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: C 195 ASN cc_start: 0.8822 (p0) cc_final: 0.8567 (p0) REVERT: C 201 ILE cc_start: 0.8875 (tt) cc_final: 0.8613 (tt) REVERT: C 384 TYR cc_start: 0.8627 (m-80) cc_final: 0.8405 (m-80) REVERT: C 486 TYR cc_start: 0.8617 (m-80) cc_final: 0.8224 (m-80) REVERT: D 641 ILE cc_start: 0.8296 (mp) cc_final: 0.7867 (tt) REVERT: D 645 LEU cc_start: 0.8620 (mt) cc_final: 0.8302 (mt) REVERT: D 656 ASN cc_start: 0.9253 (m-40) cc_final: 0.8984 (m-40) REVERT: E 69 TRP cc_start: 0.8579 (m100) cc_final: 0.8357 (m100) REVERT: E 103 GLN cc_start: 0.8845 (tt0) cc_final: 0.7966 (tp40) REVERT: E 107 ASP cc_start: 0.8830 (m-30) cc_final: 0.8264 (m-30) REVERT: E 217 TYR cc_start: 0.8027 (m-80) cc_final: 0.7150 (m-80) REVERT: E 338 TRP cc_start: 0.8838 (t-100) cc_final: 0.8349 (t-100) REVERT: E 390 LEU cc_start: 0.9560 (mt) cc_final: 0.9114 (mt) REVERT: E 426 MET cc_start: 0.8229 (mtp) cc_final: 0.7771 (mtp) REVERT: F 543 ASN cc_start: 0.8365 (m110) cc_final: 0.8094 (m110) REVERT: F 630 GLN cc_start: 0.8903 (mt0) cc_final: 0.8418 (mt0) REVERT: A 180 ASP cc_start: 0.8438 (m-30) cc_final: 0.7870 (m-30) REVERT: B 586 TYR cc_start: 0.8816 (t80) cc_final: 0.8480 (t80) REVERT: B 657 GLU cc_start: 0.9109 (tp30) cc_final: 0.8677 (tp30) REVERT: B 661 LEU cc_start: 0.5718 (mt) cc_final: 0.4819 (mt) outliers start: 5 outliers final: 1 residues processed: 303 average time/residue: 0.1242 time to fit residues: 54.9503 Evaluate side-chains 187 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 118 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 177 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 74 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN A 103 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.060028 restraints weight = 66841.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061529 restraints weight = 40864.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062529 restraints weight = 29714.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.063135 restraints weight = 24049.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063570 restraints weight = 21105.272| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16226 Z= 0.208 Angle : 0.749 11.430 22245 Z= 0.370 Chirality : 0.048 0.442 2793 Planarity : 0.004 0.041 2680 Dihedral : 8.702 72.671 3986 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.59 (0.20), residues: 1666 helix: 1.39 (0.25), residues: 421 sheet: 0.59 (0.23), residues: 431 loop : -0.17 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 500 TYR 0.021 0.002 TYR B 638 PHE 0.022 0.002 PHE E 53 TRP 0.031 0.002 TRP D 631 HIS 0.006 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00451 (16098) covalent geometry : angle 0.70372 (21894) SS BOND : bond 0.00424 ( 33) SS BOND : angle 0.95021 ( 66) hydrogen bonds : bond 0.05353 ( 591) hydrogen bonds : angle 4.89338 ( 2202) link_ALPHA1-3 : bond 0.01096 ( 3) link_ALPHA1-3 : angle 1.99396 ( 9) link_ALPHA1-6 : bond 0.00747 ( 3) link_ALPHA1-6 : angle 2.06403 ( 9) link_BETA1-4 : bond 0.00574 ( 24) link_BETA1-4 : angle 1.76388 ( 72) link_NAG-ASN : bond 0.00457 ( 65) link_NAG-ASN : angle 2.55109 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.462 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: C 195 ASN cc_start: 0.8882 (p0) cc_final: 0.8484 (p0) REVERT: C 201 ILE cc_start: 0.8877 (tt) cc_final: 0.8649 (tt) REVERT: C 317 PHE cc_start: 0.9041 (t80) cc_final: 0.8830 (t80) REVERT: C 390 LEU cc_start: 0.9377 (mt) cc_final: 0.9141 (mt) REVERT: C 486 TYR cc_start: 0.8777 (m-80) cc_final: 0.8270 (m-80) REVERT: D 577 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8138 (tm-30) REVERT: D 639 THR cc_start: 0.8689 (m) cc_final: 0.7634 (p) REVERT: D 645 LEU cc_start: 0.8692 (mt) cc_final: 0.8468 (mt) REVERT: D 656 ASN cc_start: 0.9109 (m-40) cc_final: 0.8791 (m110) REVERT: E 104 MET cc_start: 0.8584 (tpp) cc_final: 0.7768 (tpp) REVERT: E 109 ILE cc_start: 0.9132 (mm) cc_final: 0.8861 (mm) REVERT: E 180 ASP cc_start: 0.9286 (m-30) cc_final: 0.8900 (m-30) REVERT: E 217 TYR cc_start: 0.7972 (m-80) cc_final: 0.7346 (m-80) REVERT: E 338 TRP cc_start: 0.9050 (t-100) cc_final: 0.8157 (t-100) REVERT: E 390 LEU cc_start: 0.9608 (mt) cc_final: 0.9016 (mt) REVERT: F 543 ASN cc_start: 0.8482 (m110) cc_final: 0.8146 (m110) REVERT: F 626 MET cc_start: 0.8111 (tpp) cc_final: 0.7682 (tpp) REVERT: A 131 CYS cc_start: 0.6213 (m) cc_final: 0.5764 (m) REVERT: A 180 ASP cc_start: 0.8511 (m-30) cc_final: 0.7939 (m-30) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.1157 time to fit residues: 43.7088 Evaluate side-chains 183 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 130 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 50.0000 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.057719 restraints weight = 68368.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.059222 restraints weight = 41435.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060209 restraints weight = 30025.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060887 restraints weight = 24396.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.061289 restraints weight = 21240.669| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16226 Z= 0.257 Angle : 0.792 15.266 22245 Z= 0.387 Chirality : 0.050 0.553 2793 Planarity : 0.005 0.055 2680 Dihedral : 8.485 64.823 3986 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.20), residues: 1666 helix: 1.08 (0.25), residues: 425 sheet: 0.27 (0.23), residues: 443 loop : -0.47 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 419 TYR 0.028 0.003 TYR C 217 PHE 0.019 0.002 PHE E 53 TRP 0.039 0.002 TRP F 631 HIS 0.011 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00564 (16098) covalent geometry : angle 0.73954 (21894) SS BOND : bond 0.00597 ( 33) SS BOND : angle 1.20521 ( 66) hydrogen bonds : bond 0.05192 ( 591) hydrogen bonds : angle 4.91559 ( 2202) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 2.67978 ( 9) link_ALPHA1-6 : bond 0.00833 ( 3) link_ALPHA1-6 : angle 2.28132 ( 9) link_BETA1-4 : bond 0.00404 ( 24) link_BETA1-4 : angle 1.70180 ( 72) link_NAG-ASN : bond 0.00494 ( 65) link_NAG-ASN : angle 2.83014 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.542 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: C 161 MET cc_start: 0.8370 (tpp) cc_final: 0.8147 (tmm) REVERT: C 307 ILE cc_start: 0.9518 (tp) cc_final: 0.9242 (tp) REVERT: D 639 THR cc_start: 0.8729 (m) cc_final: 0.7159 (m) REVERT: D 645 LEU cc_start: 0.8744 (mt) cc_final: 0.8326 (mt) REVERT: D 656 ASN cc_start: 0.9099 (m-40) cc_final: 0.8820 (m110) REVERT: E 95 MET cc_start: 0.8560 (ttp) cc_final: 0.8341 (ttp) REVERT: E 104 MET cc_start: 0.8547 (tpp) cc_final: 0.8026 (tpp) REVERT: E 217 TYR cc_start: 0.7990 (m-80) cc_final: 0.6547 (m-80) REVERT: E 338 TRP cc_start: 0.8999 (t-100) cc_final: 0.8055 (t-100) REVERT: E 390 LEU cc_start: 0.9616 (mt) cc_final: 0.8969 (mt) REVERT: E 434 MET cc_start: 0.9059 (mtp) cc_final: 0.8853 (mtp) REVERT: A 131 CYS cc_start: 0.6314 (m) cc_final: 0.5679 (m) REVERT: A 180 ASP cc_start: 0.8570 (m-30) cc_final: 0.8059 (m-30) REVERT: B 643 TYR cc_start: 0.8875 (m-10) cc_final: 0.8572 (m-10) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1232 time to fit residues: 41.4059 Evaluate side-chains 166 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 7 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 540 GLN D 625 ASN E 103 GLN F 585 HIS ** A 195 ASN ** 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 = 0.3368 r_free = 0.3368 target = 0.074249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.059748 restraints weight = 66086.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061243 restraints weight = 40118.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062290 restraints weight = 29114.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062920 restraints weight = 23513.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063232 restraints weight = 20515.212| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16226 Z= 0.138 Angle : 0.679 12.900 22245 Z= 0.328 Chirality : 0.047 0.337 2793 Planarity : 0.004 0.051 2680 Dihedral : 7.692 61.064 3986 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.33 (0.20), residues: 1666 helix: 1.46 (0.26), residues: 419 sheet: 0.33 (0.24), residues: 436 loop : -0.44 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 503 TYR 0.018 0.002 TYR D 638 PHE 0.018 0.002 PHE A 53 TRP 0.024 0.002 TRP F 631 HIS 0.008 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00302 (16098) covalent geometry : angle 0.62472 (21894) SS BOND : bond 0.00262 ( 33) SS BOND : angle 1.37105 ( 66) hydrogen bonds : bond 0.04553 ( 591) hydrogen bonds : angle 4.59120 ( 2202) link_ALPHA1-3 : bond 0.01138 ( 3) link_ALPHA1-3 : angle 2.12316 ( 9) link_ALPHA1-6 : bond 0.00974 ( 3) link_ALPHA1-6 : angle 1.81633 ( 9) link_BETA1-4 : bond 0.00481 ( 24) link_BETA1-4 : angle 1.46741 ( 72) link_NAG-ASN : bond 0.00408 ( 65) link_NAG-ASN : angle 2.63965 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8334 (tpp) cc_final: 0.8052 (tmm) REVERT: D 577 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 639 THR cc_start: 0.8898 (m) cc_final: 0.7778 (p) REVERT: D 645 LEU cc_start: 0.8667 (mt) cc_final: 0.8266 (mt) REVERT: D 656 ASN cc_start: 0.9082 (m-40) cc_final: 0.8870 (m-40) REVERT: E 49 GLU cc_start: 0.8507 (pm20) cc_final: 0.8299 (pt0) REVERT: E 95 MET cc_start: 0.8335 (ttp) cc_final: 0.7733 (tmm) REVERT: E 104 MET cc_start: 0.8601 (tpp) cc_final: 0.8071 (tpp) REVERT: E 109 ILE cc_start: 0.9068 (mm) cc_final: 0.8850 (mm) REVERT: E 217 TYR cc_start: 0.8033 (m-80) cc_final: 0.6411 (m-80) REVERT: E 390 LEU cc_start: 0.9577 (mt) cc_final: 0.9207 (mt) REVERT: F 571 TRP cc_start: 0.8166 (t60) cc_final: 0.7677 (t60) REVERT: F 596 TRP cc_start: 0.8247 (m-10) cc_final: 0.7867 (m-10) REVERT: F 626 MET cc_start: 0.8027 (tpp) cc_final: 0.7611 (tpp) REVERT: F 646 LEU cc_start: 0.9226 (mt) cc_final: 0.8670 (mm) REVERT: F 647 GLU cc_start: 0.8982 (pp20) cc_final: 0.8770 (pp20) REVERT: F 654 GLU cc_start: 0.8562 (tt0) cc_final: 0.8007 (tp30) REVERT: A 39 TYR cc_start: 0.7935 (m-80) cc_final: 0.7688 (m-10) REVERT: A 69 TRP cc_start: 0.8647 (m100) cc_final: 0.8429 (m-90) REVERT: A 131 CYS cc_start: 0.6057 (m) cc_final: 0.5429 (m) REVERT: A 180 ASP cc_start: 0.8546 (m-30) cc_final: 0.8054 (m-30) REVERT: B 542 ARG cc_start: 0.8571 (ptm160) cc_final: 0.8309 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1168 time to fit residues: 41.7202 Evaluate side-chains 176 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 171 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 168 optimal weight: 40.0000 chunk 93 optimal weight: 0.2980 chunk 117 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058289 restraints weight = 66316.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.059717 restraints weight = 41115.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.060712 restraints weight = 30174.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061311 restraints weight = 24551.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.061709 restraints weight = 21552.980| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16226 Z= 0.212 Angle : 0.747 11.414 22245 Z= 0.359 Chirality : 0.048 0.452 2793 Planarity : 0.004 0.052 2680 Dihedral : 7.632 56.697 3986 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: 0.10 (0.20), residues: 1666 helix: 1.37 (0.26), residues: 418 sheet: 0.00 (0.23), residues: 442 loop : -0.53 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.034 0.002 TYR D 643 PHE 0.017 0.002 PHE A 53 TRP 0.024 0.002 TRP A 35 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00464 (16098) covalent geometry : angle 0.69661 (21894) SS BOND : bond 0.00390 ( 33) SS BOND : angle 1.19633 ( 66) hydrogen bonds : bond 0.04763 ( 591) hydrogen bonds : angle 4.70914 ( 2202) link_ALPHA1-3 : bond 0.00921 ( 3) link_ALPHA1-3 : angle 2.51415 ( 9) link_ALPHA1-6 : bond 0.01106 ( 3) link_ALPHA1-6 : angle 2.26002 ( 9) link_BETA1-4 : bond 0.00516 ( 24) link_BETA1-4 : angle 1.53083 ( 72) link_NAG-ASN : bond 0.00739 ( 65) link_NAG-ASN : angle 2.71164 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8705 (ttm) cc_final: 0.8015 (tpp) REVERT: D 577 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8266 (tm-30) REVERT: D 639 THR cc_start: 0.8761 (m) cc_final: 0.7641 (m) REVERT: D 643 TYR cc_start: 0.8448 (m-80) cc_final: 0.8136 (m-80) REVERT: D 645 LEU cc_start: 0.8679 (mt) cc_final: 0.8295 (mt) REVERT: D 656 ASN cc_start: 0.9046 (m-40) cc_final: 0.8823 (m-40) REVERT: E 95 MET cc_start: 0.8535 (ttp) cc_final: 0.7978 (tmm) REVERT: E 104 MET cc_start: 0.8589 (tpp) cc_final: 0.8131 (tpp) REVERT: E 109 ILE cc_start: 0.9123 (mm) cc_final: 0.8912 (mm) REVERT: E 161 MET cc_start: 0.8354 (tpp) cc_final: 0.8071 (tpp) REVERT: E 217 TYR cc_start: 0.8054 (m-80) cc_final: 0.6337 (m-80) REVERT: E 390 LEU cc_start: 0.9594 (mt) cc_final: 0.9385 (mm) REVERT: E 434 MET cc_start: 0.8869 (mtp) cc_final: 0.8418 (mtm) REVERT: F 626 MET cc_start: 0.8073 (tpp) cc_final: 0.7792 (tpp) REVERT: F 654 GLU cc_start: 0.8558 (tt0) cc_final: 0.8180 (pt0) REVERT: A 35 TRP cc_start: 0.8369 (m100) cc_final: 0.8117 (m100) REVERT: A 131 CYS cc_start: 0.6231 (m) cc_final: 0.5722 (m) REVERT: A 180 ASP cc_start: 0.8497 (m-30) cc_final: 0.7983 (m-30) REVERT: B 643 TYR cc_start: 0.8948 (m-10) cc_final: 0.8647 (m-80) REVERT: B 661 LEU cc_start: 0.5572 (mt) cc_final: 0.5278 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1111 time to fit residues: 37.5589 Evaluate side-chains 162 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 177 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 126 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN F 585 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** 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 = 0.3387 r_free = 0.3387 target = 0.075064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.060506 restraints weight = 64902.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061986 restraints weight = 39963.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.063012 restraints weight = 29140.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063610 restraints weight = 23668.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064055 restraints weight = 20807.710| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16226 Z= 0.126 Angle : 0.680 14.825 22245 Z= 0.324 Chirality : 0.049 0.786 2793 Planarity : 0.004 0.044 2680 Dihedral : 7.602 99.748 3986 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.26 (0.20), residues: 1666 helix: 1.50 (0.26), residues: 415 sheet: 0.20 (0.24), residues: 427 loop : -0.47 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.023 0.002 TYR D 643 PHE 0.018 0.002 PHE E 53 TRP 0.022 0.002 TRP C 45 HIS 0.009 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00260 (16098) covalent geometry : angle 0.63459 (21894) SS BOND : bond 0.00212 ( 33) SS BOND : angle 0.99488 ( 66) hydrogen bonds : bond 0.04293 ( 591) hydrogen bonds : angle 4.50950 ( 2202) link_ALPHA1-3 : bond 0.01248 ( 3) link_ALPHA1-3 : angle 2.03519 ( 9) link_ALPHA1-6 : bond 0.01045 ( 3) link_ALPHA1-6 : angle 1.84847 ( 9) link_BETA1-4 : bond 0.00564 ( 24) link_BETA1-4 : angle 1.38742 ( 72) link_NAG-ASN : bond 0.00592 ( 65) link_NAG-ASN : angle 2.47098 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8617 (ttm) cc_final: 0.7939 (tpp) REVERT: C 195 ASN cc_start: 0.8589 (p0) cc_final: 0.8378 (p0) REVERT: C 217 TYR cc_start: 0.7689 (m-10) cc_final: 0.5730 (m-10) REVERT: C 307 ILE cc_start: 0.9306 (tp) cc_final: 0.8945 (tt) REVERT: D 577 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8172 (tm-30) REVERT: D 591 GLN cc_start: 0.9022 (tt0) cc_final: 0.8388 (tt0) REVERT: D 639 THR cc_start: 0.8664 (m) cc_final: 0.7891 (p) REVERT: D 645 LEU cc_start: 0.8529 (mt) cc_final: 0.8271 (mt) REVERT: D 656 ASN cc_start: 0.9064 (m-40) cc_final: 0.8671 (m-40) REVERT: E 69 TRP cc_start: 0.8506 (m-90) cc_final: 0.7649 (m-90) REVERT: E 95 MET cc_start: 0.8338 (ttp) cc_final: 0.7808 (tmm) REVERT: E 104 MET cc_start: 0.8534 (tpp) cc_final: 0.8023 (tpp) REVERT: E 161 MET cc_start: 0.8326 (tpp) cc_final: 0.8072 (tpp) REVERT: E 217 TYR cc_start: 0.8014 (m-80) cc_final: 0.6175 (m-80) REVERT: E 390 LEU cc_start: 0.9569 (mt) cc_final: 0.9208 (mt) REVERT: E 434 MET cc_start: 0.8815 (mtp) cc_final: 0.8429 (mtm) REVERT: F 571 TRP cc_start: 0.7804 (t60) cc_final: 0.7539 (t60) REVERT: F 596 TRP cc_start: 0.8132 (m-10) cc_final: 0.7921 (m-10) REVERT: F 626 MET cc_start: 0.8041 (tpp) cc_final: 0.7790 (tpp) REVERT: F 646 LEU cc_start: 0.9199 (mt) cc_final: 0.8661 (mm) REVERT: F 654 GLU cc_start: 0.8510 (tt0) cc_final: 0.8163 (pt0) REVERT: A 131 CYS cc_start: 0.6111 (m) cc_final: 0.5483 (m) REVERT: A 180 ASP cc_start: 0.8498 (m-30) cc_final: 0.8007 (m-30) REVERT: B 643 TYR cc_start: 0.8880 (m-10) cc_final: 0.8584 (m-80) REVERT: B 655 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8373 (pttp) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1111 time to fit residues: 40.0167 Evaluate side-chains 178 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 169 optimal weight: 40.0000 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.073019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058516 restraints weight = 67245.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059966 restraints weight = 41555.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060919 restraints weight = 30352.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.061575 restraints weight = 24745.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061984 restraints weight = 21649.352| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16226 Z= 0.209 Angle : 0.726 13.847 22245 Z= 0.349 Chirality : 0.049 0.551 2793 Planarity : 0.004 0.051 2680 Dihedral : 8.040 120.696 3986 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.01 (0.20), residues: 1666 helix: 1.39 (0.26), residues: 418 sheet: -0.11 (0.23), residues: 462 loop : -0.62 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 273 TYR 0.021 0.002 TYR E 217 PHE 0.021 0.002 PHE E 53 TRP 0.028 0.002 TRP C 45 HIS 0.010 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00462 (16098) covalent geometry : angle 0.66695 (21894) SS BOND : bond 0.00373 ( 33) SS BOND : angle 1.64332 ( 66) hydrogen bonds : bond 0.04483 ( 591) hydrogen bonds : angle 4.61870 ( 2202) link_ALPHA1-3 : bond 0.00872 ( 3) link_ALPHA1-3 : angle 2.40335 ( 9) link_ALPHA1-6 : bond 0.00864 ( 3) link_ALPHA1-6 : angle 2.11481 ( 9) link_BETA1-4 : bond 0.00416 ( 24) link_BETA1-4 : angle 1.50739 ( 72) link_NAG-ASN : bond 0.00481 ( 65) link_NAG-ASN : angle 2.83089 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.8785 (ttm) cc_final: 0.8519 (ttm) REVERT: C 161 MET cc_start: 0.8434 (tpp) cc_final: 0.8131 (tmm) REVERT: C 195 ASN cc_start: 0.8820 (p0) cc_final: 0.8543 (p0) REVERT: C 217 TYR cc_start: 0.7952 (m-10) cc_final: 0.7122 (m-10) REVERT: C 307 ILE cc_start: 0.9440 (tp) cc_final: 0.9072 (tt) REVERT: D 577 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 639 THR cc_start: 0.8638 (m) cc_final: 0.7691 (p) REVERT: D 645 LEU cc_start: 0.8620 (mt) cc_final: 0.8418 (mt) REVERT: D 656 ASN cc_start: 0.9068 (m-40) cc_final: 0.8824 (m-40) REVERT: E 69 TRP cc_start: 0.8935 (m-90) cc_final: 0.8328 (m-10) REVERT: E 109 ILE cc_start: 0.9133 (mm) cc_final: 0.8910 (mm) REVERT: E 161 MET cc_start: 0.8401 (tpp) cc_final: 0.8057 (tpp) REVERT: E 217 TYR cc_start: 0.8128 (m-80) cc_final: 0.7567 (m-80) REVERT: E 390 LEU cc_start: 0.9617 (mt) cc_final: 0.9411 (mm) REVERT: E 434 MET cc_start: 0.8918 (mtp) cc_final: 0.8636 (mtm) REVERT: F 571 TRP cc_start: 0.7893 (t60) cc_final: 0.7653 (t60) REVERT: F 596 TRP cc_start: 0.8298 (m-10) cc_final: 0.7953 (m-10) REVERT: F 626 MET cc_start: 0.8054 (tpp) cc_final: 0.7837 (tpp) REVERT: F 654 GLU cc_start: 0.8498 (tt0) cc_final: 0.8259 (pt0) REVERT: A 131 CYS cc_start: 0.6166 (m) cc_final: 0.5693 (m) REVERT: A 180 ASP cc_start: 0.8502 (m-30) cc_final: 0.7970 (m-30) REVERT: B 643 TYR cc_start: 0.9004 (m-10) cc_final: 0.8729 (m-80) REVERT: B 661 LEU cc_start: 0.5726 (mt) cc_final: 0.5115 (mt) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1087 time to fit residues: 36.4801 Evaluate side-chains 164 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 170 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 543 ASN D 625 ASN E 283 ASN F 585 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 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 = 0.3385 r_free = 0.3385 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.060769 restraints weight = 65693.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062261 restraints weight = 40384.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063287 restraints weight = 29372.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063966 restraints weight = 23759.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064339 restraints weight = 20680.749| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16226 Z= 0.121 Angle : 0.667 10.758 22245 Z= 0.320 Chirality : 0.047 0.577 2793 Planarity : 0.004 0.047 2680 Dihedral : 7.049 81.511 3986 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.11 (0.21), residues: 1666 helix: 1.46 (0.26), residues: 418 sheet: 0.08 (0.24), residues: 444 loop : -0.63 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 503 TYR 0.017 0.002 TYR D 643 PHE 0.017 0.001 PHE E 53 TRP 0.026 0.001 TRP C 45 HIS 0.010 0.001 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00255 (16098) covalent geometry : angle 0.61759 (21894) SS BOND : bond 0.00238 ( 33) SS BOND : angle 1.50718 ( 66) hydrogen bonds : bond 0.04236 ( 591) hydrogen bonds : angle 4.47706 ( 2202) link_ALPHA1-3 : bond 0.01058 ( 3) link_ALPHA1-3 : angle 1.87098 ( 9) link_ALPHA1-6 : bond 0.00869 ( 3) link_ALPHA1-6 : angle 1.82248 ( 9) link_BETA1-4 : bond 0.00523 ( 24) link_BETA1-4 : angle 1.39656 ( 72) link_NAG-ASN : bond 0.00543 ( 65) link_NAG-ASN : angle 2.48887 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.475 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: C 195 ASN cc_start: 0.8830 (p0) cc_final: 0.8498 (p0) REVERT: D 577 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 591 GLN cc_start: 0.9062 (tt0) cc_final: 0.8304 (tt0) REVERT: D 639 THR cc_start: 0.8739 (m) cc_final: 0.7614 (p) REVERT: D 643 TYR cc_start: 0.8601 (m-80) cc_final: 0.8143 (m-80) REVERT: D 656 ASN cc_start: 0.9053 (m-40) cc_final: 0.8700 (m-40) REVERT: E 104 MET cc_start: 0.8819 (mmm) cc_final: 0.8227 (tpp) REVERT: E 217 TYR cc_start: 0.7660 (m-80) cc_final: 0.7246 (m-10) REVERT: E 390 LEU cc_start: 0.9577 (mt) cc_final: 0.9194 (mt) REVERT: E 426 MET cc_start: 0.7996 (mtp) cc_final: 0.7574 (mtp) REVERT: E 434 MET cc_start: 0.8917 (mtp) cc_final: 0.8625 (mtm) REVERT: E 452 LEU cc_start: 0.9359 (mt) cc_final: 0.9023 (tp) REVERT: F 626 MET cc_start: 0.8124 (tpp) cc_final: 0.7831 (tpp) REVERT: F 654 GLU cc_start: 0.8505 (tt0) cc_final: 0.8262 (pt0) REVERT: A 131 CYS cc_start: 0.5940 (m) cc_final: 0.5381 (m) REVERT: A 180 ASP cc_start: 0.8565 (m-30) cc_final: 0.8038 (m-30) REVERT: B 643 TYR cc_start: 0.8882 (m-10) cc_final: 0.8637 (m-80) REVERT: B 661 LEU cc_start: 0.5704 (mt) cc_final: 0.5123 (mt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1094 time to fit residues: 38.3002 Evaluate side-chains 176 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 30.0000 chunk 107 optimal weight: 0.0060 chunk 84 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 177 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN A 249 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 653 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 = 0.3313 r_free = 0.3313 target = 0.071701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057279 restraints weight = 67408.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058742 restraints weight = 41212.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059708 restraints weight = 29869.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060380 restraints weight = 24258.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.060737 restraints weight = 21103.819| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16226 Z= 0.280 Angle : 0.801 11.474 22245 Z= 0.387 Chirality : 0.048 0.244 2793 Planarity : 0.004 0.052 2680 Dihedral : 7.151 54.625 3986 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 (0.20), residues: 1666 helix: 1.07 (0.26), residues: 419 sheet: -0.26 (0.23), residues: 446 loop : -0.85 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 588 TYR 0.030 0.003 TYR D 643 PHE 0.023 0.002 PHE C 53 TRP 0.044 0.003 TRP C 45 HIS 0.012 0.002 HIS F 585 Details of bonding type rmsd covalent geometry : bond 0.00622 (16098) covalent geometry : angle 0.75500 (21894) SS BOND : bond 0.00513 ( 33) SS BOND : angle 1.07697 ( 66) hydrogen bonds : bond 0.04750 ( 591) hydrogen bonds : angle 4.77147 ( 2202) link_ALPHA1-3 : bond 0.00688 ( 3) link_ALPHA1-3 : angle 2.28226 ( 9) link_ALPHA1-6 : bond 0.00674 ( 3) link_ALPHA1-6 : angle 2.05957 ( 9) link_BETA1-4 : bond 0.00448 ( 24) link_BETA1-4 : angle 1.59592 ( 72) link_NAG-ASN : bond 0.00572 ( 65) link_NAG-ASN : angle 2.72874 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.532 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: C 195 ASN cc_start: 0.8896 (p0) cc_final: 0.8571 (p0) REVERT: C 390 LEU cc_start: 0.9246 (mt) cc_final: 0.9012 (mt) REVERT: C 475 MET cc_start: 0.8325 (mmm) cc_final: 0.8116 (mmm) REVERT: D 577 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 639 THR cc_start: 0.8523 (m) cc_final: 0.7192 (p) REVERT: D 643 TYR cc_start: 0.8633 (m-80) cc_final: 0.8111 (m-80) REVERT: D 656 ASN cc_start: 0.8993 (m-40) cc_final: 0.8702 (m110) REVERT: E 42 VAL cc_start: 0.8427 (t) cc_final: 0.8089 (m) REVERT: E 104 MET cc_start: 0.8865 (mmm) cc_final: 0.8564 (tpp) REVERT: E 217 TYR cc_start: 0.7950 (m-80) cc_final: 0.7645 (m-80) REVERT: E 434 MET cc_start: 0.8928 (mtp) cc_final: 0.8669 (mtm) REVERT: E 452 LEU cc_start: 0.9328 (mt) cc_final: 0.8985 (tp) REVERT: F 626 MET cc_start: 0.8035 (tpp) cc_final: 0.7804 (tpp) REVERT: F 654 GLU cc_start: 0.8534 (tt0) cc_final: 0.8272 (pt0) REVERT: A 131 CYS cc_start: 0.5932 (m) cc_final: 0.5630 (m) REVERT: A 180 ASP cc_start: 0.8586 (m-30) cc_final: 0.8038 (m-30) REVERT: B 643 TYR cc_start: 0.8968 (m-10) cc_final: 0.8753 (m-80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0969 time to fit residues: 31.6122 Evaluate side-chains 151 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN D 625 ASN D 650 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 653 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 = 0.3365 r_free = 0.3365 target = 0.074116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.059851 restraints weight = 65011.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.061299 restraints weight = 40161.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062280 restraints weight = 29265.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062925 restraints weight = 23749.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063313 restraints weight = 20724.887| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16226 Z= 0.127 Angle : 0.678 10.779 22245 Z= 0.327 Chirality : 0.046 0.244 2793 Planarity : 0.004 0.051 2680 Dihedral : 7.452 120.444 3986 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.08 (0.20), residues: 1666 helix: 1.38 (0.27), residues: 418 sheet: 0.00 (0.24), residues: 427 loop : -0.81 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 298 TYR 0.028 0.002 TYR C 217 PHE 0.020 0.002 PHE E 53 TRP 0.029 0.002 TRP C 45 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00277 (16098) covalent geometry : angle 0.63191 (21894) SS BOND : bond 0.00508 ( 33) SS BOND : angle 1.13415 ( 66) hydrogen bonds : bond 0.04321 ( 591) hydrogen bonds : angle 4.54350 ( 2202) link_ALPHA1-3 : bond 0.00908 ( 3) link_ALPHA1-3 : angle 1.56768 ( 9) link_ALPHA1-6 : bond 0.00795 ( 3) link_ALPHA1-6 : angle 2.02737 ( 9) link_BETA1-4 : bond 0.00494 ( 24) link_BETA1-4 : angle 1.34878 ( 72) link_NAG-ASN : bond 0.00488 ( 65) link_NAG-ASN : angle 2.48657 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.04 seconds wall clock time: 38 minutes 2.93 seconds (2282.93 seconds total)