Starting phenix.real_space_refine on Mon Apr 6 05:12:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8g_23233/04_2026/7l8g_23233.map" } resolution = 4.3 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= 0.002 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 9826 2.51 5 N 2656 2.21 5 O 3218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15802 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3512 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 952 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3497 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 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: 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: "R" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" 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: "E" 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: "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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 3.86, per 1000 atoms: 0.24 Number of scatterers: 15802 At special positions: 0 Unit cell: (130.81, 125.66, 145.23, 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 3218 8.00 N 2656 7.00 C 9826 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=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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=2.07 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 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=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Y 3 " - " MAN Y 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 701 " - " ASN A 276 " " NAG A 702 " - " ASN A 386 " " NAG A 703 " - " ASN A 363 " " NAG A 704 " - " ASN A 234 " " NAG A 705 " - " ASN A 133 " " NAG A 706 " - " ASN A 289 " " NAG A 707 " - " ASN A 339 " " NAG A 708 " - " ASN A 355 " " NAG A 709 " - " 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 301 " " NAG C 707 " - " ASN C 289 " " NAG C 708 " - " ASN C 339 " " NAG C 709 " - " ASN C 355 " " NAG C 710 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " 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 289 " " NAG E 709 " - " ASN E 339 " " NAG E 710 " - " ASN E 355 " " NAG E 711 " - " ASN E 392 " " 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 88 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 295 " " NAG U 1 " - " ASN E 197 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 241 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 160 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 587.5 milliseconds 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 45 sheets defined 27.7% alpha, 80.1% 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 99 through 117 removed outlier: 4.010A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (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 351 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.726A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 546 removed outlier: 3.719A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 4.515A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) 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 139 through 151 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.618A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.138A 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 425 through 429 Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'E' and resid 479 through 484 Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.839A pdb=" N LYS F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 4.428A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 656 removed outlier: 3.855A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.611A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.236A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.854A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.926A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.917A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.385A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.029A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.421A 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: 6.648A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.843A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.695A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.370A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.291A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.478A 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 56 removed outlier: 5.054A pdb=" N ILE E 215 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY E 250 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR E 217 " --> pdb=" O THR E 248 " (cutoff:3.500A) 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 removed outlier: 3.728A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 3.708A pdb=" N MET E 434 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A 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: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A 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: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A 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: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A 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: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A 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: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.395A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.100A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AE3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AE4, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.524A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.548A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.659A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AE7, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.615A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AE9, first strand: chain 'L' and resid 11 through 12 removed outlier: 4.051A pdb=" N UNK L 102 " --> pdb=" O UNK L 11 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK L 45 " --> pdb=" O UNK L 37 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2262 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: 3.53 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4070 1.33 - 1.47: 4938 1.47 - 1.61: 6917 1.61 - 1.75: 24 1.75 - 1.89: 124 Bond restraints: 16073 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.52e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 16068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19640 2.81 - 5.62: 2018 5.62 - 8.43: 189 8.43 - 11.24: 13 11.24 - 14.05: 3 Bond angle restraints: 21863 Sorted by residual: angle pdb=" N THR C 320 " pdb=" CA THR C 320 " pdb=" C THR C 320 " ideal model delta sigma weight residual 112.54 122.84 -10.30 1.22e+00 6.72e-01 7.13e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.01e+00 9.80e-01 7.11e+01 angle pdb=" N ILE E 424 " pdb=" CA ILE E 424 " pdb=" C ILE E 424 " ideal model delta sigma weight residual 108.11 119.66 -11.55 1.40e+00 5.10e-01 6.81e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.56 -8.00 1.01e+00 9.80e-01 6.28e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.70 101.84 8.86 1.22e+00 6.72e-01 5.28e+01 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 10583 21.32 - 42.65: 218 42.65 - 63.97: 73 63.97 - 85.29: 31 85.29 - 106.61: 15 Dihedral angle restraints: 10920 sinusoidal: 5403 harmonic: 5517 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.02 46.02 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -41.57 -44.43 1 1.00e+01 1.00e-02 2.74e+01 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 -130.05 44.05 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 2441 0.247 - 0.494: 349 0.494 - 0.740: 9 0.740 - 0.987: 0 0.987 - 1.234: 1 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2797 not shown) Planarity restraints: 2734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " -0.350 2.00e-02 2.50e+03 3.01e-01 1.14e+03 pdb=" C7 NAG F 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " 0.347 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 702 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 708 " 0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A 708 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 708 " 0.050 2.00e-02 2.50e+03 pdb=" N2 NAG A 708 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG A 708 " 0.198 2.00e-02 2.50e+03 ... (remaining 2731 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5183 2.86 - 3.37: 14782 3.37 - 3.88: 26497 3.88 - 4.39: 30686 4.39 - 4.90: 47198 Nonbonded interactions: 124346 Sorted by model distance: nonbonded pdb=" N LEU F 523 " pdb=" OE1 GLN F 540 " model vdw 2.354 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP E 368 " pdb=" N LEU E 369 " model vdw 2.424 3.120 nonbonded pdb=" NZ LYS A 335 " pdb=" OD2 ASP A 412 " model vdw 2.439 3.120 nonbonded pdb=" N PRO E 437 " pdb=" O PRO E 437 " model vdw 2.439 2.496 ... (remaining 124341 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 505 or resid 701 through 709)) selection = (chain 'C' and (resid 33 through 58 or resid 66 through 397 or resid 411 through \ 505 or resid 701 through 709)) selection = (chain 'E' and (resid 33 through 58 or resid 66 through 505 or resid 702 through \ 710)) } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 11 through 110) 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 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.940 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 0.131 16204 Z= 1.220 Angle : 1.797 14.048 22223 Z= 1.117 Chirality : 0.156 1.234 2800 Planarity : 0.016 0.301 2670 Dihedral : 11.312 106.613 7233 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.64 (0.20), residues: 1659 helix: -0.69 (0.23), residues: 421 sheet: 1.04 (0.23), residues: 438 loop : 0.94 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 192 TYR 0.041 0.008 TYR E 173 PHE 0.035 0.006 PHE E 353 TRP 0.070 0.010 TRP C 35 HIS 0.017 0.003 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02243 (16073) covalent geometry : angle 1.75565 (21863) SS BOND : bond 0.02068 ( 33) SS BOND : angle 2.49710 ( 66) hydrogen bonds : bond 0.17122 ( 543) hydrogen bonds : angle 7.95219 ( 2262) link_ALPHA1-3 : bond 0.09268 ( 3) link_ALPHA1-3 : angle 4.61297 ( 9) link_ALPHA1-6 : bond 0.06407 ( 3) link_ALPHA1-6 : angle 3.60954 ( 9) link_BETA1-4 : bond 0.07208 ( 28) link_BETA1-4 : angle 4.81597 ( 84) link_NAG-ASN : bond 0.07665 ( 64) link_NAG-ASN : angle 2.95850 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.548 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: C 39 TYR cc_start: 0.8791 (m-80) cc_final: 0.8404 (m-80) REVERT: C 453 ILE cc_start: 0.9234 (mt) cc_final: 0.8924 (tt) REVERT: D 543 ASN cc_start: 0.9127 (m-40) cc_final: 0.8908 (m110) REVERT: D 571 TRP cc_start: 0.6646 (t60) cc_final: 0.6201 (t60) REVERT: D 588 ARG cc_start: 0.9167 (mmm160) cc_final: 0.8921 (tpp-160) REVERT: E 129 LEU cc_start: 0.9176 (mt) cc_final: 0.8949 (mt) REVERT: E 166 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8370 (mtp85) REVERT: E 338 TRP cc_start: 0.8699 (t-100) cc_final: 0.8493 (t-100) REVERT: F 523 LEU cc_start: 0.9266 (mt) cc_final: 0.8922 (mt) REVERT: F 536 THR cc_start: 0.8788 (p) cc_final: 0.8556 (t) REVERT: F 584 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9030 (mt-10) REVERT: F 590 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8760 (tm-30) REVERT: F 591 GLN cc_start: 0.9440 (tt0) cc_final: 0.8921 (tt0) REVERT: F 630 GLN cc_start: 0.9445 (mt0) cc_final: 0.9019 (mt0) REVERT: F 634 GLU cc_start: 0.8623 (tp30) cc_final: 0.8276 (tt0) REVERT: F 638 TYR cc_start: 0.7927 (m-80) cc_final: 0.7591 (m-80) REVERT: F 648 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8946 (tm-30) REVERT: F 656 ASN cc_start: 0.9152 (m-40) cc_final: 0.8783 (m-40) REVERT: A 47 ASP cc_start: 0.8793 (m-30) cc_final: 0.8557 (p0) REVERT: B 536 THR cc_start: 0.8871 (p) cc_final: 0.8648 (p) REVERT: B 584 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8902 (tm-30) REVERT: B 585 HIS cc_start: 0.8873 (m-70) cc_final: 0.8604 (m-70) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1361 time to fit residues: 78.7388 Evaluate side-chains 210 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN C 114 GLN C 195 ASN C 302 ASN C 352 HIS C 374 HIS D 630 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050048 restraints weight = 74213.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.051546 restraints weight = 44291.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052560 restraints weight = 31257.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.053259 restraints weight = 24732.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053609 restraints weight = 21064.406| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16204 Z= 0.196 Angle : 0.838 10.012 22223 Z= 0.411 Chirality : 0.050 0.319 2800 Planarity : 0.004 0.037 2670 Dihedral : 8.707 87.104 4041 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.46 % Allowed : 2.38 % Favored : 97.16 % 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: 0.60 (0.20), residues: 1659 helix: 0.23 (0.25), residues: 404 sheet: 0.67 (0.22), residues: 470 loop : 0.51 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 617 TYR 0.026 0.002 TYR B 643 PHE 0.016 0.002 PHE C 53 TRP 0.023 0.002 TRP C 479 HIS 0.010 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00426 (16073) covalent geometry : angle 0.77475 (21863) SS BOND : bond 0.00253 ( 33) SS BOND : angle 1.48617 ( 66) hydrogen bonds : bond 0.06458 ( 543) hydrogen bonds : angle 4.94398 ( 2262) link_ALPHA1-3 : bond 0.01258 ( 3) link_ALPHA1-3 : angle 1.68611 ( 9) link_ALPHA1-6 : bond 0.00719 ( 3) link_ALPHA1-6 : angle 1.70261 ( 9) link_BETA1-4 : bond 0.00770 ( 28) link_BETA1-4 : angle 2.54946 ( 84) link_NAG-ASN : bond 0.00626 ( 64) link_NAG-ASN : angle 2.99599 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 270 time to evaluate : 0.444 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 39 TYR cc_start: 0.8411 (m-80) cc_final: 0.7988 (m-80) REVERT: C 150 MET cc_start: 0.7849 (mmm) cc_final: 0.7545 (mmt) REVERT: C 218 CYS cc_start: 0.6799 (m) cc_final: 0.6541 (m) REVERT: C 333 VAL cc_start: 0.9147 (t) cc_final: 0.8912 (m) REVERT: C 453 ILE cc_start: 0.9254 (mt) cc_final: 0.9054 (tt) REVERT: C 475 MET cc_start: 0.8902 (mmp) cc_final: 0.8649 (mmp) REVERT: D 543 ASN cc_start: 0.8818 (m-40) cc_final: 0.8482 (m110) REVERT: D 626 MET cc_start: 0.6917 (mtp) cc_final: 0.6448 (mtp) REVERT: D 653 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8859 (mm110) REVERT: E 104 MET cc_start: 0.8855 (ttt) cc_final: 0.8536 (ttt) REVERT: E 195 ASN cc_start: 0.8158 (t0) cc_final: 0.7871 (t0) REVERT: E 338 TRP cc_start: 0.8643 (t-100) cc_final: 0.8418 (t-100) REVERT: F 522 PHE cc_start: 0.8358 (t80) cc_final: 0.7908 (t80) REVERT: F 530 MET cc_start: 0.8926 (mtt) cc_final: 0.8633 (mtt) REVERT: F 536 THR cc_start: 0.8584 (p) cc_final: 0.8283 (t) REVERT: F 588 ARG cc_start: 0.8833 (tmm-80) cc_final: 0.8577 (tmm-80) REVERT: F 599 SER cc_start: 0.9244 (p) cc_final: 0.8836 (m) REVERT: F 601 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9093 (mtpt) REVERT: F 630 GLN cc_start: 0.9484 (mt0) cc_final: 0.9104 (mt0) REVERT: A 53 PHE cc_start: 0.8007 (m-10) cc_final: 0.7732 (m-10) REVERT: A 104 MET cc_start: 0.8401 (tpt) cc_final: 0.6800 (tpt) REVERT: A 125 LEU cc_start: 0.9462 (mp) cc_final: 0.9134 (mt) REVERT: A 161 MET cc_start: 0.9004 (tpp) cc_final: 0.8689 (tpp) REVERT: A 166 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8105 (ttm110) REVERT: A 217 TYR cc_start: 0.8073 (m-10) cc_final: 0.7613 (m-10) REVERT: A 368 ASP cc_start: 0.8377 (p0) cc_final: 0.6985 (p0) REVERT: A 370 GLU cc_start: 0.8776 (mp0) cc_final: 0.8338 (mp0) REVERT: A 452 LEU cc_start: 0.9333 (mp) cc_final: 0.9085 (mp) REVERT: B 523 LEU cc_start: 0.9153 (mt) cc_final: 0.8769 (mt) REVERT: B 584 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8918 (tm-30) REVERT: B 586 TYR cc_start: 0.9100 (t80) cc_final: 0.8875 (t80) REVERT: B 601 LYS cc_start: 0.9076 (pttm) cc_final: 0.8742 (ptpp) REVERT: B 626 MET cc_start: 0.7617 (tpp) cc_final: 0.7166 (tpp) REVERT: B 630 GLN cc_start: 0.9049 (mt0) cc_final: 0.8715 (mt0) outliers start: 7 outliers final: 0 residues processed: 273 average time/residue: 0.1312 time to fit residues: 52.7145 Evaluate side-chains 198 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 148 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 GLN E 170 GLN A 82 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 570 HIS B 585 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048641 restraints weight = 75883.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050065 restraints weight = 45253.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.051049 restraints weight = 32212.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.051671 restraints weight = 25680.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052036 restraints weight = 22100.443| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16204 Z= 0.175 Angle : 0.690 8.769 22223 Z= 0.345 Chirality : 0.046 0.249 2800 Planarity : 0.004 0.044 2670 Dihedral : 7.529 77.160 4041 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.26 % Allowed : 3.04 % Favored : 96.70 % 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: 0.37 (0.20), residues: 1659 helix: 0.31 (0.26), residues: 396 sheet: 0.49 (0.22), residues: 470 loop : 0.22 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 579 TYR 0.016 0.002 TYR B 643 PHE 0.033 0.002 PHE D 522 TRP 0.018 0.002 TRP C 479 HIS 0.008 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00382 (16073) covalent geometry : angle 0.65097 (21863) SS BOND : bond 0.00239 ( 33) SS BOND : angle 1.39534 ( 66) hydrogen bonds : bond 0.05104 ( 543) hydrogen bonds : angle 4.43283 ( 2262) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 2.14032 ( 9) link_ALPHA1-6 : bond 0.01144 ( 3) link_ALPHA1-6 : angle 1.79603 ( 9) link_BETA1-4 : bond 0.00544 ( 28) link_BETA1-4 : angle 1.74540 ( 84) link_NAG-ASN : bond 0.00336 ( 64) link_NAG-ASN : angle 2.13092 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 236 time to evaluate : 0.597 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: C 39 TYR cc_start: 0.8553 (m-80) cc_final: 0.7927 (m-80) REVERT: C 382 PHE cc_start: 0.8787 (m-80) cc_final: 0.8508 (m-80) REVERT: C 453 ILE cc_start: 0.9354 (mt) cc_final: 0.9153 (tt) REVERT: D 569 THR cc_start: 0.5978 (p) cc_final: 0.5716 (p) REVERT: D 626 MET cc_start: 0.7876 (mtp) cc_final: 0.7541 (mtp) REVERT: D 653 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8901 (mm110) REVERT: E 104 MET cc_start: 0.8934 (ttt) cc_final: 0.8509 (ttt) REVERT: E 452 LEU cc_start: 0.9470 (mp) cc_final: 0.8931 (tp) REVERT: F 522 PHE cc_start: 0.8339 (t80) cc_final: 0.7973 (t80) REVERT: F 536 THR cc_start: 0.8582 (p) cc_final: 0.8314 (t) REVERT: F 588 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8605 (tmm-80) REVERT: F 630 GLN cc_start: 0.9451 (mt0) cc_final: 0.9069 (mt0) REVERT: F 638 TYR cc_start: 0.7928 (m-10) cc_final: 0.7707 (m-10) REVERT: F 654 GLU cc_start: 0.9155 (tp30) cc_final: 0.8830 (tp30) REVERT: A 53 PHE cc_start: 0.7995 (m-10) cc_final: 0.7783 (m-10) REVERT: A 104 MET cc_start: 0.8542 (tpt) cc_final: 0.8318 (tpt) REVERT: A 161 MET cc_start: 0.9063 (tpp) cc_final: 0.8605 (tpp) REVERT: A 166 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8204 (ttm110) REVERT: A 368 ASP cc_start: 0.8243 (p0) cc_final: 0.6756 (p0) REVERT: A 370 GLU cc_start: 0.8697 (mp0) cc_final: 0.8265 (mp0) REVERT: B 523 LEU cc_start: 0.9180 (mt) cc_final: 0.8942 (mt) REVERT: B 584 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8875 (tm-30) REVERT: B 601 LYS cc_start: 0.9145 (pttm) cc_final: 0.8848 (ptpp) REVERT: B 626 MET cc_start: 0.7624 (tpp) cc_final: 0.7219 (tpp) REVERT: B 630 GLN cc_start: 0.9088 (mt0) cc_final: 0.8792 (mt0) outliers start: 4 outliers final: 0 residues processed: 238 average time/residue: 0.1310 time to fit residues: 45.6554 Evaluate side-chains 173 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 180 optimal weight: 50.0000 chunk 163 optimal weight: 20.0000 chunk 171 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.046376 restraints weight = 76409.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047719 restraints weight = 46283.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.048640 restraints weight = 33206.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.049278 restraints weight = 26667.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.049669 restraints weight = 23069.830| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 16204 Z= 0.300 Angle : 0.810 9.937 22223 Z= 0.398 Chirality : 0.049 0.261 2800 Planarity : 0.005 0.060 2670 Dihedral : 7.751 72.975 4041 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.55 % 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: 1659 helix: -0.07 (0.26), residues: 408 sheet: 0.25 (0.22), residues: 469 loop : -0.06 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 298 TYR 0.032 0.002 TYR C 217 PHE 0.023 0.003 PHE D 522 TRP 0.017 0.002 TRP C 479 HIS 0.006 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00652 (16073) covalent geometry : angle 0.77230 (21863) SS BOND : bond 0.00463 ( 33) SS BOND : angle 1.62952 ( 66) hydrogen bonds : bond 0.05435 ( 543) hydrogen bonds : angle 4.60273 ( 2262) link_ALPHA1-3 : bond 0.00801 ( 3) link_ALPHA1-3 : angle 2.56328 ( 9) link_ALPHA1-6 : bond 0.01567 ( 3) link_ALPHA1-6 : angle 2.05136 ( 9) link_BETA1-4 : bond 0.00531 ( 28) link_BETA1-4 : angle 1.72021 ( 84) link_NAG-ASN : bond 0.00509 ( 64) link_NAG-ASN : angle 2.31978 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 0.606 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 39 TYR cc_start: 0.8679 (m-80) cc_final: 0.7921 (m-80) REVERT: C 382 PHE cc_start: 0.8893 (m-80) cc_final: 0.8543 (m-80) REVERT: D 626 MET cc_start: 0.7930 (mtp) cc_final: 0.7625 (mtp) REVERT: E 50 THR cc_start: 0.9124 (t) cc_final: 0.8912 (p) REVERT: E 368 ASP cc_start: 0.8508 (p0) cc_final: 0.8230 (p0) REVERT: E 475 MET cc_start: 0.9008 (mmm) cc_final: 0.8774 (mmm) REVERT: F 535 MET cc_start: 0.8112 (mpp) cc_final: 0.7898 (mpp) REVERT: A 114 GLN cc_start: 0.9077 (tp40) cc_final: 0.8839 (tp40) REVERT: A 150 MET cc_start: 0.9044 (mmm) cc_final: 0.8820 (mpp) REVERT: B 584 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8957 (tm-30) REVERT: B 601 LYS cc_start: 0.9147 (pttm) cc_final: 0.8849 (ptpp) REVERT: B 625 ASN cc_start: 0.8733 (m-40) cc_final: 0.8058 (m-40) REVERT: B 626 MET cc_start: 0.7613 (tpp) cc_final: 0.7182 (mmm) REVERT: B 635 ILE cc_start: 0.9209 (pt) cc_final: 0.8942 (pt) REVERT: B 654 GLU cc_start: 0.9008 (tp30) cc_final: 0.8232 (pt0) outliers start: 4 outliers final: 1 residues processed: 199 average time/residue: 0.1378 time to fit residues: 39.8832 Evaluate side-chains 153 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 169 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 575 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048285 restraints weight = 74265.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049598 restraints weight = 45571.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050534 restraints weight = 33062.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051056 restraints weight = 26557.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051527 restraints weight = 23203.584| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 16204 Z= 0.137 Angle : 0.659 13.751 22223 Z= 0.325 Chirality : 0.046 0.349 2800 Planarity : 0.003 0.043 2670 Dihedral : 7.088 68.692 4041 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.02 % 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: 1659 helix: 0.25 (0.26), residues: 398 sheet: 0.35 (0.23), residues: 457 loop : -0.09 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.029 0.001 TYR C 217 PHE 0.017 0.001 PHE C 53 TRP 0.013 0.001 TRP A 395 HIS 0.007 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00306 (16073) covalent geometry : angle 0.61733 (21863) SS BOND : bond 0.00257 ( 33) SS BOND : angle 1.55959 ( 66) hydrogen bonds : bond 0.04670 ( 543) hydrogen bonds : angle 4.26357 ( 2262) link_ALPHA1-3 : bond 0.00939 ( 3) link_ALPHA1-3 : angle 2.24804 ( 9) link_ALPHA1-6 : bond 0.01363 ( 3) link_ALPHA1-6 : angle 1.80503 ( 9) link_BETA1-4 : bond 0.00511 ( 28) link_BETA1-4 : angle 1.51141 ( 84) link_NAG-ASN : bond 0.00315 ( 64) link_NAG-ASN : angle 2.14044 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.530 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 39 TYR cc_start: 0.8649 (m-80) cc_final: 0.7821 (m-80) REVERT: C 217 TYR cc_start: 0.7808 (m-80) cc_final: 0.7583 (m-10) REVERT: C 382 PHE cc_start: 0.8735 (m-80) cc_final: 0.8448 (m-80) REVERT: C 443 ILE cc_start: 0.8824 (tp) cc_final: 0.8583 (tt) REVERT: D 626 MET cc_start: 0.7804 (mtp) cc_final: 0.7575 (mtp) REVERT: E 95 MET cc_start: 0.8937 (ptm) cc_final: 0.8133 (ppp) REVERT: E 195 ASN cc_start: 0.7926 (t0) cc_final: 0.7644 (t0) REVERT: E 368 ASP cc_start: 0.8532 (p0) cc_final: 0.8272 (p0) REVERT: E 452 LEU cc_start: 0.9412 (mp) cc_final: 0.8935 (tp) REVERT: E 475 MET cc_start: 0.9028 (mmm) cc_final: 0.8761 (mmm) REVERT: F 530 MET cc_start: 0.8352 (pmm) cc_final: 0.7975 (pmm) REVERT: F 588 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8551 (tmm-80) REVERT: F 599 SER cc_start: 0.9200 (p) cc_final: 0.8891 (m) REVERT: F 626 MET cc_start: 0.7737 (tpp) cc_final: 0.7521 (mmm) REVERT: A 112 TRP cc_start: 0.8612 (t-100) cc_final: 0.8348 (t-100) REVERT: A 125 LEU cc_start: 0.9498 (mp) cc_final: 0.9114 (mt) REVERT: A 161 MET cc_start: 0.9081 (tpp) cc_final: 0.8688 (tpp) REVERT: A 166 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7975 (ttm110) REVERT: A 217 TYR cc_start: 0.8139 (m-10) cc_final: 0.7242 (m-10) REVERT: A 425 ASN cc_start: 0.8442 (m-40) cc_final: 0.8232 (m-40) REVERT: B 584 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8892 (tm-30) REVERT: B 601 LYS cc_start: 0.9151 (pttm) cc_final: 0.8866 (ptpp) REVERT: B 633 LYS cc_start: 0.9668 (mmmm) cc_final: 0.9455 (mmmm) REVERT: B 654 GLU cc_start: 0.8915 (tp30) cc_final: 0.8326 (pt0) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1311 time to fit residues: 40.4681 Evaluate side-chains 163 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 182 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 585 HIS A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.047863 restraints weight = 76309.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049232 restraints weight = 45635.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050205 restraints weight = 32874.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050869 restraints weight = 26231.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.051283 restraints weight = 22650.251| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 16204 Z= 0.168 Angle : 0.700 17.921 22223 Z= 0.344 Chirality : 0.047 0.338 2800 Planarity : 0.004 0.042 2670 Dihedral : 6.986 66.652 4041 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.02 (0.20), residues: 1659 helix: 0.16 (0.26), residues: 399 sheet: 0.30 (0.23), residues: 445 loop : -0.09 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.028 0.001 TYR C 217 PHE 0.013 0.001 PHE C 53 TRP 0.012 0.001 TRP D 631 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00383 (16073) covalent geometry : angle 0.65068 (21863) SS BOND : bond 0.00503 ( 33) SS BOND : angle 2.38287 ( 66) hydrogen bonds : bond 0.04709 ( 543) hydrogen bonds : angle 4.21993 ( 2262) link_ALPHA1-3 : bond 0.00955 ( 3) link_ALPHA1-3 : angle 2.31498 ( 9) link_ALPHA1-6 : bond 0.01329 ( 3) link_ALPHA1-6 : angle 1.86788 ( 9) link_BETA1-4 : bond 0.00402 ( 28) link_BETA1-4 : angle 1.53071 ( 84) link_NAG-ASN : bond 0.00482 ( 64) link_NAG-ASN : angle 2.26621 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.578 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 39 TYR cc_start: 0.8692 (m-80) cc_final: 0.7865 (m-80) REVERT: C 217 TYR cc_start: 0.7760 (m-80) cc_final: 0.7374 (m-80) REVERT: C 382 PHE cc_start: 0.8789 (m-80) cc_final: 0.8469 (m-80) REVERT: C 443 ILE cc_start: 0.8858 (tp) cc_final: 0.8611 (tt) REVERT: E 95 MET cc_start: 0.8937 (ptm) cc_final: 0.8187 (ppp) REVERT: E 99 ASN cc_start: 0.8842 (m-40) cc_final: 0.8567 (t0) REVERT: E 161 MET cc_start: 0.8693 (tpp) cc_final: 0.8451 (tpt) REVERT: E 195 ASN cc_start: 0.7865 (t0) cc_final: 0.7628 (t0) REVERT: E 368 ASP cc_start: 0.8607 (p0) cc_final: 0.8345 (p0) REVERT: E 452 LEU cc_start: 0.9423 (mp) cc_final: 0.9001 (tp) REVERT: E 475 MET cc_start: 0.9004 (mmm) cc_final: 0.8753 (mmm) REVERT: F 530 MET cc_start: 0.8368 (pmm) cc_final: 0.8162 (pmm) REVERT: F 588 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8563 (tmm-80) REVERT: F 599 SER cc_start: 0.9263 (p) cc_final: 0.8965 (m) REVERT: F 647 GLU cc_start: 0.9163 (pm20) cc_final: 0.8922 (pm20) REVERT: A 150 MET cc_start: 0.8713 (mpp) cc_final: 0.8339 (mpp) REVERT: A 166 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8136 (ttm110) REVERT: B 542 ARG cc_start: 0.8454 (tpt170) cc_final: 0.8249 (tpt170) REVERT: B 584 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8896 (tm-30) REVERT: B 601 LYS cc_start: 0.9206 (pttm) cc_final: 0.8924 (ptpp) REVERT: B 631 TRP cc_start: 0.9257 (t-100) cc_final: 0.8859 (t-100) REVERT: B 633 LYS cc_start: 0.9761 (mmmm) cc_final: 0.9519 (mmmm) REVERT: B 635 ILE cc_start: 0.9169 (pt) cc_final: 0.8840 (pt) REVERT: B 654 GLU cc_start: 0.8835 (tp30) cc_final: 0.8294 (mp0) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1308 time to fit residues: 38.9535 Evaluate side-chains 158 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 178 optimal weight: 40.0000 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 478 ASN D 575 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.047329 restraints weight = 74818.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.048689 restraints weight = 45075.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049587 restraints weight = 32214.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050222 restraints weight = 25978.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.050589 restraints weight = 22289.610| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16204 Z= 0.197 Angle : 0.697 16.431 22223 Z= 0.344 Chirality : 0.047 0.317 2800 Planarity : 0.004 0.043 2670 Dihedral : 7.030 63.816 4041 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.06 (0.20), residues: 1659 helix: 0.15 (0.26), residues: 398 sheet: 0.27 (0.23), residues: 467 loop : -0.19 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 298 TYR 0.019 0.002 TYR B 643 PHE 0.012 0.002 PHE C 53 TRP 0.015 0.002 TRP D 631 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00443 (16073) covalent geometry : angle 0.65319 (21863) SS BOND : bond 0.00465 ( 33) SS BOND : angle 2.04456 ( 66) hydrogen bonds : bond 0.04741 ( 543) hydrogen bonds : angle 4.21477 ( 2262) link_ALPHA1-3 : bond 0.00858 ( 3) link_ALPHA1-3 : angle 2.45415 ( 9) link_ALPHA1-6 : bond 0.01336 ( 3) link_ALPHA1-6 : angle 1.86345 ( 9) link_BETA1-4 : bond 0.00361 ( 28) link_BETA1-4 : angle 1.46670 ( 84) link_NAG-ASN : bond 0.00416 ( 64) link_NAG-ASN : angle 2.18818 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.579 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 39 TYR cc_start: 0.8748 (m-80) cc_final: 0.7929 (m-80) REVERT: C 382 PHE cc_start: 0.8782 (m-80) cc_final: 0.8494 (m-80) REVERT: C 443 ILE cc_start: 0.8915 (tp) cc_final: 0.8652 (tt) REVERT: D 574 LYS cc_start: 0.9022 (pttp) cc_final: 0.8656 (pttp) REVERT: D 645 LEU cc_start: 0.9173 (mp) cc_final: 0.8889 (tp) REVERT: E 161 MET cc_start: 0.8672 (tpp) cc_final: 0.8434 (tpt) REVERT: E 195 ASN cc_start: 0.7949 (t0) cc_final: 0.7681 (t0) REVERT: E 368 ASP cc_start: 0.8696 (p0) cc_final: 0.8473 (p0) REVERT: E 452 LEU cc_start: 0.9401 (mp) cc_final: 0.8994 (tp) REVERT: E 475 MET cc_start: 0.8791 (mmm) cc_final: 0.8307 (mmm) REVERT: F 530 MET cc_start: 0.8369 (pmm) cc_final: 0.8151 (pmm) REVERT: F 591 GLN cc_start: 0.9250 (tt0) cc_final: 0.8983 (tt0) REVERT: F 599 SER cc_start: 0.9293 (p) cc_final: 0.9004 (m) REVERT: F 626 MET cc_start: 0.7812 (tpp) cc_final: 0.7551 (tpp) REVERT: F 630 GLN cc_start: 0.9411 (mt0) cc_final: 0.9031 (mt0) REVERT: A 150 MET cc_start: 0.8640 (mpp) cc_final: 0.8338 (mpp) REVERT: A 166 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8121 (ttm110) REVERT: B 584 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8905 (tm-30) REVERT: B 601 LYS cc_start: 0.9178 (pttm) cc_final: 0.8977 (ptpp) REVERT: B 626 MET cc_start: 0.6184 (tpt) cc_final: 0.5073 (tpt) REVERT: B 633 LYS cc_start: 0.9807 (mmmm) cc_final: 0.9544 (mmmm) REVERT: B 635 ILE cc_start: 0.9090 (pt) cc_final: 0.8822 (pt) REVERT: B 654 GLU cc_start: 0.8876 (tp30) cc_final: 0.8233 (pt0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1385 time to fit residues: 39.7211 Evaluate side-chains 149 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 575 GLN E 293 GLN A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.047777 restraints weight = 75277.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049128 restraints weight = 45361.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050087 restraints weight = 32555.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050726 restraints weight = 25946.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.051058 restraints weight = 22329.859| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16204 Z= 0.145 Angle : 0.661 16.505 22223 Z= 0.325 Chirality : 0.046 0.280 2800 Planarity : 0.003 0.041 2670 Dihedral : 6.806 61.400 4041 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.02 (0.20), residues: 1659 helix: 0.30 (0.27), residues: 398 sheet: 0.30 (0.23), residues: 455 loop : -0.23 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.031 0.001 TYR C 217 PHE 0.013 0.001 PHE C 53 TRP 0.022 0.001 TRP B 631 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00332 (16073) covalent geometry : angle 0.61882 (21863) SS BOND : bond 0.00477 ( 33) SS BOND : angle 1.93456 ( 66) hydrogen bonds : bond 0.04511 ( 543) hydrogen bonds : angle 4.11028 ( 2262) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 2.32894 ( 9) link_ALPHA1-6 : bond 0.01378 ( 3) link_ALPHA1-6 : angle 1.87150 ( 9) link_BETA1-4 : bond 0.00382 ( 28) link_BETA1-4 : angle 1.39324 ( 84) link_NAG-ASN : bond 0.00350 ( 64) link_NAG-ASN : angle 2.09642 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.584 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: C 39 TYR cc_start: 0.8764 (m-80) cc_final: 0.7934 (m-80) REVERT: C 194 ILE cc_start: 0.9424 (pt) cc_final: 0.9223 (pt) REVERT: C 382 PHE cc_start: 0.8747 (m-80) cc_final: 0.8510 (m-80) REVERT: C 426 MET cc_start: 0.8601 (tpt) cc_final: 0.8175 (tpp) REVERT: C 434 MET cc_start: 0.8446 (mtm) cc_final: 0.8226 (mtt) REVERT: C 443 ILE cc_start: 0.8818 (tp) cc_final: 0.8545 (tt) REVERT: C 475 MET cc_start: 0.8260 (mmm) cc_final: 0.7385 (mmm) REVERT: C 479 TRP cc_start: 0.9237 (m-90) cc_final: 0.8522 (m-90) REVERT: D 574 LYS cc_start: 0.9027 (pttp) cc_final: 0.8657 (pttp) REVERT: D 645 LEU cc_start: 0.9140 (mp) cc_final: 0.8933 (tp) REVERT: E 95 MET cc_start: 0.8967 (ptm) cc_final: 0.7961 (ppp) REVERT: E 161 MET cc_start: 0.8722 (tpp) cc_final: 0.8484 (tpt) REVERT: E 195 ASN cc_start: 0.7799 (t0) cc_final: 0.7591 (t0) REVERT: E 293 GLN cc_start: 0.8724 (tt0) cc_final: 0.8424 (tm-30) REVERT: F 530 MET cc_start: 0.8366 (pmm) cc_final: 0.8125 (pmm) REVERT: F 588 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8591 (tmm-80) REVERT: F 591 GLN cc_start: 0.9218 (tt0) cc_final: 0.8955 (tt0) REVERT: F 599 SER cc_start: 0.9313 (p) cc_final: 0.9021 (m) REVERT: F 648 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8718 (tm-30) REVERT: A 150 MET cc_start: 0.8602 (mpp) cc_final: 0.8399 (mpp) REVERT: A 166 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8113 (ttm110) REVERT: B 584 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8856 (tm-30) REVERT: B 654 GLU cc_start: 0.8986 (tp30) cc_final: 0.8218 (pt0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1311 time to fit residues: 40.3129 Evaluate side-chains 157 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 181 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 478 ASN D 575 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046995 restraints weight = 76492.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.048354 restraints weight = 46339.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.049262 restraints weight = 33288.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049881 restraints weight = 26814.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050272 restraints weight = 23211.742| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16204 Z= 0.209 Angle : 0.724 16.087 22223 Z= 0.356 Chirality : 0.047 0.283 2800 Planarity : 0.004 0.044 2670 Dihedral : 7.022 59.234 4041 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: -0.12 (0.21), residues: 1659 helix: 0.13 (0.26), residues: 405 sheet: 0.24 (0.24), residues: 447 loop : -0.25 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 298 TYR 0.031 0.002 TYR C 217 PHE 0.021 0.002 PHE A 53 TRP 0.020 0.002 TRP B 631 HIS 0.009 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00470 (16073) covalent geometry : angle 0.68361 (21863) SS BOND : bond 0.00581 ( 33) SS BOND : angle 2.13000 ( 66) hydrogen bonds : bond 0.04720 ( 543) hydrogen bonds : angle 4.20953 ( 2262) link_ALPHA1-3 : bond 0.00796 ( 3) link_ALPHA1-3 : angle 2.44408 ( 9) link_ALPHA1-6 : bond 0.01436 ( 3) link_ALPHA1-6 : angle 1.85200 ( 9) link_BETA1-4 : bond 0.00357 ( 28) link_BETA1-4 : angle 1.45174 ( 84) link_NAG-ASN : bond 0.00402 ( 64) link_NAG-ASN : angle 2.14610 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8780 (m-80) cc_final: 0.7940 (m-80) REVERT: C 426 MET cc_start: 0.8586 (tpt) cc_final: 0.8216 (tpp) REVERT: C 443 ILE cc_start: 0.8873 (tp) cc_final: 0.8579 (tt) REVERT: D 542 ARG cc_start: 0.8260 (ptp-170) cc_final: 0.7954 (ptt-90) REVERT: D 574 LYS cc_start: 0.9061 (pttp) cc_final: 0.8658 (pttp) REVERT: D 596 TRP cc_start: 0.8846 (m-10) cc_final: 0.8503 (m-10) REVERT: D 645 LEU cc_start: 0.9145 (mp) cc_final: 0.8909 (tp) REVERT: E 95 MET cc_start: 0.8889 (ptm) cc_final: 0.8136 (ppp) REVERT: E 195 ASN cc_start: 0.7990 (t0) cc_final: 0.7713 (t0) REVERT: E 293 GLN cc_start: 0.8777 (tt0) cc_final: 0.8459 (tm-30) REVERT: F 530 MET cc_start: 0.8382 (pmm) cc_final: 0.8079 (pmm) REVERT: F 599 SER cc_start: 0.9311 (p) cc_final: 0.9079 (m) REVERT: F 626 MET cc_start: 0.7962 (tpp) cc_final: 0.7760 (tpp) REVERT: A 166 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8155 (ttm110) REVERT: A 217 TYR cc_start: 0.8024 (m-10) cc_final: 0.7529 (m-10) REVERT: B 584 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8860 (tm-30) REVERT: B 654 GLU cc_start: 0.9004 (tp30) cc_final: 0.8268 (pt0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1333 time to fit residues: 37.7400 Evaluate side-chains 142 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 173 optimal weight: 30.0000 chunk 85 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 575 GLN A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.061473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.047944 restraints weight = 75858.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049317 restraints weight = 45663.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050214 restraints weight = 32788.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050829 restraints weight = 26530.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.050836 restraints weight = 22693.833| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16204 Z= 0.159 Angle : 0.684 16.180 22223 Z= 0.339 Chirality : 0.047 0.300 2800 Planarity : 0.004 0.043 2670 Dihedral : 6.860 57.049 4041 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.12 (0.21), residues: 1659 helix: 0.16 (0.27), residues: 400 sheet: 0.28 (0.23), residues: 469 loop : -0.30 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.027 0.001 TYR C 217 PHE 0.014 0.001 PHE C 53 TRP 0.030 0.001 TRP B 631 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00367 (16073) covalent geometry : angle 0.64397 (21863) SS BOND : bond 0.00518 ( 33) SS BOND : angle 1.91333 ( 66) hydrogen bonds : bond 0.04486 ( 543) hydrogen bonds : angle 4.12614 ( 2262) link_ALPHA1-3 : bond 0.00850 ( 3) link_ALPHA1-3 : angle 2.31544 ( 9) link_ALPHA1-6 : bond 0.01377 ( 3) link_ALPHA1-6 : angle 1.88071 ( 9) link_BETA1-4 : bond 0.00372 ( 28) link_BETA1-4 : angle 1.38479 ( 84) link_NAG-ASN : bond 0.00560 ( 64) link_NAG-ASN : angle 2.10462 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8816 (m-80) cc_final: 0.7891 (m-80) REVERT: C 104 MET cc_start: 0.7621 (mmt) cc_final: 0.6667 (mmt) REVERT: C 426 MET cc_start: 0.8517 (tpt) cc_final: 0.8171 (tpp) REVERT: C 443 ILE cc_start: 0.8817 (tp) cc_final: 0.8543 (tt) REVERT: C 475 MET cc_start: 0.8347 (mmm) cc_final: 0.7775 (mmm) REVERT: C 479 TRP cc_start: 0.9266 (m-90) cc_final: 0.8417 (m-90) REVERT: D 538 THR cc_start: 0.9298 (p) cc_final: 0.9039 (m) REVERT: D 574 LYS cc_start: 0.9050 (pttp) cc_final: 0.8641 (pttp) REVERT: D 596 TRP cc_start: 0.8829 (m-10) cc_final: 0.8484 (m-10) REVERT: D 645 LEU cc_start: 0.9121 (mp) cc_final: 0.8913 (tp) REVERT: E 161 MET cc_start: 0.8781 (tpp) cc_final: 0.8489 (tpt) REVERT: E 195 ASN cc_start: 0.7846 (t0) cc_final: 0.7573 (t0) REVERT: E 293 GLN cc_start: 0.8757 (tt0) cc_final: 0.8439 (tm-30) REVERT: F 535 MET cc_start: 0.7949 (mmm) cc_final: 0.7535 (mpp) REVERT: F 588 ARG cc_start: 0.8917 (tmm-80) cc_final: 0.8626 (tmm-80) REVERT: F 591 GLN cc_start: 0.9225 (tt0) cc_final: 0.8980 (tt0) REVERT: F 599 SER cc_start: 0.9310 (p) cc_final: 0.9087 (m) REVERT: F 632 ASP cc_start: 0.8472 (p0) cc_final: 0.8245 (p0) REVERT: F 633 LYS cc_start: 0.9402 (mttp) cc_final: 0.9196 (mptp) REVERT: A 125 LEU cc_start: 0.9574 (mp) cc_final: 0.9335 (mp) REVERT: A 161 MET cc_start: 0.9089 (tpp) cc_final: 0.8727 (tpp) REVERT: A 166 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8184 (ttm110) REVERT: A 443 ILE cc_start: 0.9164 (mm) cc_final: 0.8915 (tt) REVERT: B 584 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8847 (tm-30) REVERT: B 625 ASN cc_start: 0.7862 (m-40) cc_final: 0.7654 (m-40) REVERT: B 654 GLU cc_start: 0.9068 (tp30) cc_final: 0.8273 (pt0) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1288 time to fit residues: 37.5154 Evaluate side-chains 154 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 171 optimal weight: 50.0000 chunk 26 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 146 optimal weight: 0.2980 chunk 144 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN D 575 GLN E 170 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.047634 restraints weight = 76371.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.048969 restraints weight = 46163.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.049913 restraints weight = 33215.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050406 restraints weight = 26580.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050846 restraints weight = 23380.675| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16204 Z= 0.183 Angle : 0.711 16.002 22223 Z= 0.350 Chirality : 0.048 0.280 2800 Planarity : 0.004 0.043 2670 Dihedral : 6.886 55.037 4041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.18 (0.21), residues: 1659 helix: 0.12 (0.27), residues: 400 sheet: 0.22 (0.23), residues: 469 loop : -0.33 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 298 TYR 0.031 0.002 TYR C 217 PHE 0.010 0.002 PHE C 382 TRP 0.026 0.002 TRP A 427 HIS 0.009 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00419 (16073) covalent geometry : angle 0.67033 (21863) SS BOND : bond 0.00540 ( 33) SS BOND : angle 1.92964 ( 66) hydrogen bonds : bond 0.04493 ( 543) hydrogen bonds : angle 4.19397 ( 2262) link_ALPHA1-3 : bond 0.00800 ( 3) link_ALPHA1-3 : angle 2.30374 ( 9) link_ALPHA1-6 : bond 0.01376 ( 3) link_ALPHA1-6 : angle 1.85819 ( 9) link_BETA1-4 : bond 0.00365 ( 28) link_BETA1-4 : angle 1.41926 ( 84) link_NAG-ASN : bond 0.00485 ( 64) link_NAG-ASN : angle 2.18486 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2170.71 seconds wall clock time: 38 minutes 37.76 seconds (2317.76 seconds total)