Starting phenix.real_space_refine on Fri Jul 3 20:53:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8g_23233/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8g_23233/07_2026/7l8g_23233.cif" } 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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 4.10, per 1000 atoms: 0.26 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: 1.33 Conformation dependent library (CDL) restraints added in 482.7 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: 0.74 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: 3.48 Time building geometry restraints manager: 1.75 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 - 17.98: 8565 17.98 - 35.95: 211 35.95 - 53.93: 70 53.93 - 71.91: 22 71.91 - 89.88: 12 Dihedral angle restraints: 8880 sinusoidal: 3363 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 8877 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 16.040 Find NCS groups from input model: 0.500 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 10.272 89.884 5193 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/Z covalent geometry : bond 0.02243 / 1.19 (16073) covalent geometry : angle 1.75565 / 1.12 (21863) SS BOND : bond 0.02068 / 1.36 ( 33) SS BOND : angle 2.49710 / 1.76 ( 66) hydrogen bonds : bond 0.17122 / 11.26 ( 543) hydrogen bonds : angle 7.95219 / 5.58 ( 2262) link_ALPHA1-3 : bond 0.09268 / 4.65 ( 3) link_ALPHA1-3 : angle 4.61297 / 3.28 ( 9) link_ALPHA1-6 : bond 0.06407 / 3.23 ( 3) link_ALPHA1-6 : angle 3.60954 / 2.19 ( 9) link_BETA1-4 : bond 0.07208 / 4.33 ( 28) link_BETA1-4 : angle 4.81597 / 3.34 ( 84) link_NAG-ASN : bond 0.07665 / 4.74 ( 64) link_NAG-ASN : angle 2.95850 / 2.13 ( 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 : 0.474 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: 0.1334 time to fit residues: 77.5694 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 : 0.460 ------------------------------------------------------------------------------- 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... 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.050033 restraints weight = 74185.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.051500 restraints weight = 44267.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052520 restraints weight = 31463.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053183 restraints weight = 24891.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053696 restraints weight = 21291.052| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 16204 Z= 0.200 Angle : 0.835 10.540 22223 Z= 0.410 Chirality : 0.049 0.340 2800 Planarity : 0.004 0.039 2670 Dihedral : 5.166 29.563 2001 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.53 % Allowed : 2.45 % Favored : 97.03 % 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: 0.58 (0.20), residues: 1659 helix: 0.18 (0.25), residues: 404 sheet: 0.67 (0.22), residues: 469 loop : 0.51 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 273 TYR 0.025 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/Z covalent geometry : bond 0.00430 / 0.20 (16073) covalent geometry : angle 0.77741 / 0.40 (21863) SS BOND : bond 0.00745 / 0.45 ( 33) SS BOND : angle 1.49914 / 0.97 ( 66) hydrogen bonds : bond 0.06419 / 4.25 ( 543) hydrogen bonds : angle 4.94315 / 3.43 ( 2262) link_ALPHA1-3 : bond 0.00820 / 0.41 ( 3) link_ALPHA1-3 : angle 1.62911 / 1.08 ( 9) link_ALPHA1-6 : bond 0.00849 / 0.43 ( 3) link_ALPHA1-6 : angle 1.50665 / 1.03 ( 9) link_BETA1-4 : bond 0.00891 / 0.61 ( 28) link_BETA1-4 : angle 2.39344 / 1.65 ( 84) link_NAG-ASN : bond 0.00558 / 0.35 ( 64) link_NAG-ASN : angle 2.89811 / 2.03 ( 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 279 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 271 time to evaluate : 0.577 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: C 39 TYR cc_start: 0.8397 (m-80) cc_final: 0.7968 (m-80) REVERT: C 150 MET cc_start: 0.7911 (mmm) cc_final: 0.7633 (mmt) REVERT: C 218 CYS cc_start: 0.6786 (m) cc_final: 0.6524 (m) REVERT: C 333 VAL cc_start: 0.9145 (t) cc_final: 0.8907 (m) REVERT: C 475 MET cc_start: 0.8881 (mmp) cc_final: 0.8617 (mmp) REVERT: D 543 ASN cc_start: 0.8820 (m-40) cc_final: 0.8430 (m110) REVERT: D 653 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8863 (mm110) REVERT: E 104 MET cc_start: 0.8858 (ttt) cc_final: 0.8545 (ttt) REVERT: E 195 ASN cc_start: 0.8176 (t0) cc_final: 0.7880 (t0) REVERT: E 338 TRP cc_start: 0.8643 (t-100) cc_final: 0.8413 (t-100) REVERT: E 368 ASP cc_start: 0.8429 (p0) cc_final: 0.8175 (p0) REVERT: F 522 PHE cc_start: 0.8354 (t80) cc_final: 0.7899 (t80) REVERT: F 530 MET cc_start: 0.8974 (mtt) cc_final: 0.8681 (mtt) REVERT: F 535 MET cc_start: 0.8081 (mpp) cc_final: 0.7866 (mpp) REVERT: F 536 THR cc_start: 0.8578 (p) cc_final: 0.8280 (t) REVERT: F 588 ARG cc_start: 0.8846 (tmm-80) cc_final: 0.8590 (tmm-80) REVERT: F 599 SER cc_start: 0.9249 (p) cc_final: 0.8844 (m) REVERT: F 601 LYS cc_start: 0.9336 (mmmt) cc_final: 0.9092 (mtpt) REVERT: F 630 GLN cc_start: 0.9481 (mt0) cc_final: 0.9096 (mt0) REVERT: F 638 TYR cc_start: 0.7999 (m-80) cc_final: 0.7703 (m-10) REVERT: A 53 PHE cc_start: 0.8015 (m-10) cc_final: 0.7740 (m-10) REVERT: A 104 MET cc_start: 0.8419 (tpt) cc_final: 0.6822 (tpt) REVERT: A 125 LEU cc_start: 0.9467 (mp) cc_final: 0.9126 (mt) REVERT: A 161 MET cc_start: 0.8985 (tpp) cc_final: 0.8636 (tpp) REVERT: A 166 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8131 (ttm110) REVERT: A 217 TYR cc_start: 0.8064 (m-10) cc_final: 0.7608 (m-10) REVERT: A 368 ASP cc_start: 0.8370 (p0) cc_final: 0.8062 (p0) REVERT: A 452 LEU cc_start: 0.9332 (mp) cc_final: 0.9083 (mp) REVERT: B 523 LEU cc_start: 0.9155 (mt) cc_final: 0.8785 (mt) REVERT: B 584 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8918 (tm-30) REVERT: B 626 MET cc_start: 0.7599 (tpp) cc_final: 0.7359 (tpp) REVERT: B 630 GLN cc_start: 0.9048 (mt0) cc_final: 0.8652 (mt0) outliers start: 8 outliers final: 0 residues processed: 275 average time/residue: 0.1224 time to fit residues: 49.8426 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 : 0.522 ------------------------------------------------------------------------------- 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: 0.0570 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 27 optimal weight: 0.0030 chunk 78 optimal weight: 6.9990 overall best weight: 1.0112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 570 HIS D 575 GLN E 170 GLN A 82 GLN A 283 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 585 HIS B 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.063463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050086 restraints weight = 74251.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051564 restraints weight = 44099.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052583 restraints weight = 31041.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053243 restraints weight = 24514.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053724 restraints weight = 20929.118| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16204 Z= 0.133 Angle : 0.654 8.703 22223 Z= 0.328 Chirality : 0.045 0.238 2800 Planarity : 0.004 0.043 2670 Dihedral : 4.834 28.705 2001 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.20 % Allowed : 2.84 % Favored : 96.96 % 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: 0.39 (0.20), residues: 1659 helix: 0.22 (0.26), residues: 408 sheet: 0.61 (0.22), residues: 474 loop : 0.22 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.020 0.001 TYR B 643 PHE 0.030 0.001 PHE D 522 TRP 0.017 0.001 TRP B 623 HIS 0.008 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16073) covalent geometry : angle 0.61741 / 0.32 (21863) SS BOND : bond 0.00438 / 0.23 ( 33) SS BOND : angle 1.37390 / 0.83 ( 66) hydrogen bonds : bond 0.04987 / 3.26 ( 543) hydrogen bonds : angle 4.39978 / 3.06 ( 2262) link_ALPHA1-3 : bond 0.00552 / 0.28 ( 3) link_ALPHA1-3 : angle 1.44158 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00879 / 0.44 ( 3) link_ALPHA1-6 : angle 1.38707 / 0.97 ( 9) link_BETA1-4 : bond 0.00550 / 0.34 ( 28) link_BETA1-4 : angle 1.57672 / 1.08 ( 84) link_NAG-ASN : bond 0.00351 / 0.22 ( 64) link_NAG-ASN : angle 2.06108 / 1.44 ( 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 259 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 256 time to evaluate : 0.539 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: 0.8443 (m-80) cc_final: 0.7892 (m-80) REVERT: C 113 ASP cc_start: 0.8958 (t0) cc_final: 0.8671 (m-30) REVERT: C 150 MET cc_start: 0.7813 (mmm) cc_final: 0.7583 (mmt) REVERT: C 382 PHE cc_start: 0.8764 (m-80) cc_final: 0.8510 (m-80) REVERT: C 475 MET cc_start: 0.8898 (mmp) cc_final: 0.8695 (mmp) REVERT: D 538 THR cc_start: 0.9208 (p) cc_final: 0.8552 (p) REVERT: D 542 ARG cc_start: 0.8182 (ptp-170) cc_final: 0.7803 (ptp90) REVERT: D 626 MET cc_start: 0.7844 (mtp) cc_final: 0.7459 (mtp) REVERT: D 639 THR cc_start: 0.8705 (p) cc_final: 0.8497 (p) REVERT: D 653 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8875 (mm110) REVERT: E 95 MET cc_start: 0.8843 (ptm) cc_final: 0.7346 (ppp) REVERT: E 104 MET cc_start: 0.8941 (ttt) cc_final: 0.8518 (ttt) REVERT: E 368 ASP cc_start: 0.8396 (p0) cc_final: 0.8152 (p0) REVERT: E 452 LEU cc_start: 0.9456 (mp) cc_final: 0.8910 (tp) REVERT: F 522 PHE cc_start: 0.8322 (t80) cc_final: 0.8082 (t80) REVERT: F 523 LEU cc_start: 0.9328 (mt) cc_final: 0.9047 (mp) REVERT: F 536 THR cc_start: 0.8471 (p) cc_final: 0.8109 (t) REVERT: F 599 SER cc_start: 0.9203 (p) cc_final: 0.8749 (m) REVERT: F 630 GLN cc_start: 0.9468 (mt0) cc_final: 0.9209 (mt0) REVERT: F 632 ASP cc_start: 0.8261 (p0) cc_final: 0.8035 (p0) REVERT: F 638 TYR cc_start: 0.7899 (m-80) cc_final: 0.7651 (m-10) REVERT: F 654 GLU cc_start: 0.9135 (tp30) cc_final: 0.8816 (tp30) REVERT: A 53 PHE cc_start: 0.7937 (m-10) cc_final: 0.7717 (m-10) REVERT: A 125 LEU cc_start: 0.9474 (mp) cc_final: 0.9238 (mp) REVERT: A 161 MET cc_start: 0.9000 (tpp) cc_final: 0.8589 (tpp) REVERT: A 166 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8205 (ttm110) REVERT: A 368 ASP cc_start: 0.8233 (p0) cc_final: 0.6792 (p0) REVERT: A 370 GLU cc_start: 0.8718 (mp0) cc_final: 0.8347 (mp0) REVERT: B 523 LEU cc_start: 0.9144 (mt) cc_final: 0.8934 (mt) REVERT: B 584 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8883 (tm-30) REVERT: B 601 LYS cc_start: 0.9086 (pttm) cc_final: 0.8815 (ptpp) REVERT: B 626 MET cc_start: 0.7587 (tpp) cc_final: 0.7308 (tpp) REVERT: B 630 GLN cc_start: 0.9057 (mt0) cc_final: 0.8756 (mt0) outliers start: 3 outliers final: 0 residues processed: 258 average time/residue: 0.1271 time to fit residues: 48.4134 Evaluate side-chains 186 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 10.0000 chunk 171 optimal weight: 40.0000 chunk 158 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 ASN C 195 ASN E 170 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 283 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049593 restraints weight = 74532.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.051055 restraints weight = 44422.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052010 restraints weight = 31487.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052665 restraints weight = 25109.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053129 restraints weight = 21564.087| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16204 Z= 0.135 Angle : 0.626 8.919 22223 Z= 0.313 Chirality : 0.044 0.249 2800 Planarity : 0.003 0.040 2670 Dihedral : 4.678 31.997 2001 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.40 % Allowed : 1.92 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1659 helix: 0.24 (0.26), residues: 409 sheet: 0.52 (0.22), residues: 471 loop : 0.14 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.019 0.001 TYR C 217 PHE 0.019 0.002 PHE D 522 TRP 0.012 0.001 TRP B 623 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16073) covalent geometry : angle 0.59341 / 0.31 (21863) SS BOND : bond 0.00255 / 0.14 ( 33) SS BOND : angle 1.36058 / 0.81 ( 66) hydrogen bonds : bond 0.04546 / 2.97 ( 543) hydrogen bonds : angle 4.18399 / 2.91 ( 2262) link_ALPHA1-3 : bond 0.00434 / 0.22 ( 3) link_ALPHA1-3 : angle 1.45920 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00791 / 0.40 ( 3) link_ALPHA1-6 : angle 1.40379 / 0.99 ( 9) link_BETA1-4 : bond 0.00395 / 0.25 ( 28) link_BETA1-4 : angle 1.37361 / 0.95 ( 84) link_NAG-ASN : bond 0.00313 / 0.18 ( 64) link_NAG-ASN : angle 1.89106 / 1.33 ( 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 229 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 0.552 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: 0.8511 (m-80) cc_final: 0.7935 (m-80) REVERT: C 382 PHE cc_start: 0.8706 (m-80) cc_final: 0.8418 (m-80) REVERT: D 538 THR cc_start: 0.9248 (p) cc_final: 0.8544 (p) REVERT: D 542 ARG cc_start: 0.8250 (ptp-170) cc_final: 0.7459 (ptp90) REVERT: D 653 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8896 (mm110) REVERT: E 95 MET cc_start: 0.8881 (ptm) cc_final: 0.7438 (ppp) REVERT: E 104 MET cc_start: 0.8923 (ttt) cc_final: 0.8640 (ttm) REVERT: E 368 ASP cc_start: 0.8408 (p0) cc_final: 0.8133 (p0) REVERT: E 452 LEU cc_start: 0.9403 (mp) cc_final: 0.8954 (tp) REVERT: F 522 PHE cc_start: 0.8322 (t80) cc_final: 0.8110 (t80) REVERT: F 523 LEU cc_start: 0.9351 (mt) cc_final: 0.9092 (mp) REVERT: F 536 THR cc_start: 0.8504 (p) cc_final: 0.8213 (t) REVERT: F 657 GLU cc_start: 0.8949 (tp30) cc_final: 0.8732 (tp30) REVERT: A 112 TRP cc_start: 0.8767 (t-100) cc_final: 0.8458 (t-100) REVERT: A 150 MET cc_start: 0.8981 (mmm) cc_final: 0.8773 (mpp) REVERT: A 161 MET cc_start: 0.9063 (tpp) cc_final: 0.8691 (tpp) REVERT: A 166 ARG cc_start: 0.8393 (ttm110) cc_final: 0.7783 (ttm110) REVERT: A 368 ASP cc_start: 0.8150 (p0) cc_final: 0.6647 (p0) REVERT: A 370 GLU cc_start: 0.8713 (mp0) cc_final: 0.8334 (mp0) REVERT: B 584 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8876 (tm-30) REVERT: B 631 TRP cc_start: 0.8998 (t-100) cc_final: 0.8771 (t-100) REVERT: B 635 ILE cc_start: 0.9150 (pt) cc_final: 0.8926 (pt) REVERT: B 654 GLU cc_start: 0.8922 (tp30) cc_final: 0.8087 (pt0) outliers start: 6 outliers final: 0 residues processed: 226 average time/residue: 0.1208 time to fit residues: 40.9432 Evaluate side-chains 179 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 58 optimal weight: 10.0000 chunk 169 optimal weight: 30.0000 chunk 91 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN D 575 GLN D 585 HIS E 170 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.048911 restraints weight = 75277.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.050343 restraints weight = 45127.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.051299 restraints weight = 32126.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051973 restraints weight = 25591.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052433 restraints weight = 21914.182| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 16204 Z= 0.154 Angle : 0.640 14.162 22223 Z= 0.318 Chirality : 0.045 0.318 2800 Planarity : 0.003 0.042 2670 Dihedral : 4.652 31.968 2001 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1659 helix: 0.35 (0.27), residues: 405 sheet: 0.49 (0.23), residues: 457 loop : 0.04 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 298 TYR 0.018 0.001 TYR C 217 PHE 0.016 0.002 PHE C 53 TRP 0.011 0.001 TRP D 631 HIS 0.008 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16073) covalent geometry : angle 0.60175 / 0.31 (21863) SS BOND : bond 0.00418 / 0.23 ( 33) SS BOND : angle 1.83513 / 1.06 ( 66) hydrogen bonds : bond 0.04439 / 2.90 ( 543) hydrogen bonds : angle 4.13336 / 2.87 ( 2262) link_ALPHA1-3 : bond 0.00420 / 0.21 ( 3) link_ALPHA1-3 : angle 1.55720 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00950 / 0.49 ( 3) link_ALPHA1-6 : angle 1.46033 / 1.01 ( 9) link_BETA1-4 : bond 0.00397 / 0.24 ( 28) link_BETA1-4 : angle 1.38221 / 0.96 ( 84) link_NAG-ASN : bond 0.00482 / 0.24 ( 64) link_NAG-ASN : angle 2.00925 / 1.39 ( 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 225 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.496 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: C 39 TYR cc_start: 0.8587 (m-80) cc_final: 0.7934 (m-80) REVERT: C 382 PHE cc_start: 0.8672 (m-80) cc_final: 0.8446 (m-80) REVERT: D 574 LYS cc_start: 0.9007 (pttp) cc_final: 0.8635 (pttm) REVERT: D 626 MET cc_start: 0.7899 (mtp) cc_final: 0.7595 (mtp) REVERT: E 95 MET cc_start: 0.8881 (ptm) cc_final: 0.7529 (ppp) REVERT: E 99 ASN cc_start: 0.8800 (m-40) cc_final: 0.8376 (t0) REVERT: E 195 ASN cc_start: 0.7823 (t0) cc_final: 0.7543 (t0) REVERT: E 368 ASP cc_start: 0.8492 (p0) cc_final: 0.8193 (p0) REVERT: E 432 GLN cc_start: 0.7312 (pm20) cc_final: 0.7037 (pm20) REVERT: E 452 LEU cc_start: 0.9421 (mp) cc_final: 0.8974 (tp) REVERT: F 536 THR cc_start: 0.8593 (p) cc_final: 0.8306 (t) REVERT: F 591 GLN cc_start: 0.9191 (tt0) cc_final: 0.8937 (tt0) REVERT: F 657 GLU cc_start: 0.9001 (tp30) cc_final: 0.8733 (tp30) REVERT: A 104 MET cc_start: 0.8699 (mmm) cc_final: 0.8347 (tpt) REVERT: A 125 LEU cc_start: 0.9483 (mp) cc_final: 0.9219 (mp) REVERT: A 161 MET cc_start: 0.9064 (tpp) cc_final: 0.8645 (tpp) REVERT: A 166 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7797 (ttm110) REVERT: A 368 ASP cc_start: 0.8146 (p0) cc_final: 0.6443 (p0) REVERT: A 370 GLU cc_start: 0.8703 (mp0) cc_final: 0.8280 (mp0) REVERT: B 523 LEU cc_start: 0.9138 (mt) cc_final: 0.8845 (mt) REVERT: B 584 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8893 (tm-30) REVERT: B 601 LYS cc_start: 0.9204 (pttm) cc_final: 0.8859 (ptpp) REVERT: B 635 ILE cc_start: 0.9308 (pt) cc_final: 0.9094 (pt) REVERT: B 654 GLU cc_start: 0.9055 (tp30) cc_final: 0.8186 (pt0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1241 time to fit residues: 41.7797 Evaluate side-chains 169 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 0.0470 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN E 170 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.049490 restraints weight = 75153.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050926 restraints weight = 44889.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051871 restraints weight = 31801.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052554 restraints weight = 25430.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053026 restraints weight = 21493.023| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 16204 Z= 0.140 Angle : 0.661 17.841 22223 Z= 0.327 Chirality : 0.045 0.347 2800 Planarity : 0.003 0.043 2670 Dihedral : 4.615 30.469 2001 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 0.19 (0.20), residues: 1659 helix: 0.25 (0.27), residues: 413 sheet: 0.50 (0.23), residues: 454 loop : -0.02 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.033 0.001 TYR C 217 PHE 0.015 0.001 PHE C 53 TRP 0.012 0.001 TRP F 571 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16073) covalent geometry : angle 0.61913 / 0.32 (21863) SS BOND : bond 0.00695 / 0.35 ( 33) SS BOND : angle 2.22715 / 1.26 ( 66) hydrogen bonds : bond 0.04336 / 2.80 ( 543) hydrogen bonds : angle 4.02764 / 2.79 ( 2262) link_ALPHA1-3 : bond 0.00367 / 0.19 ( 3) link_ALPHA1-3 : angle 1.45810 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00752 / 0.38 ( 3) link_ALPHA1-6 : angle 1.42664 / 0.99 ( 9) link_BETA1-4 : bond 0.00450 / 0.26 ( 28) link_BETA1-4 : angle 1.34120 / 0.91 ( 84) link_NAG-ASN : bond 0.00519 / 0.25 ( 64) link_NAG-ASN : angle 2.05228 / 1.40 ( 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 222 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.604 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: 0.8577 (m-80) cc_final: 0.7857 (m-80) REVERT: C 104 MET cc_start: 0.8527 (mmp) cc_final: 0.8171 (mmt) REVERT: C 382 PHE cc_start: 0.8775 (m-80) cc_final: 0.8447 (m-80) REVERT: D 574 LYS cc_start: 0.9009 (pttp) cc_final: 0.8653 (pttp) REVERT: D 626 MET cc_start: 0.7823 (mtp) cc_final: 0.7552 (mtp) REVERT: E 95 MET cc_start: 0.8874 (ptm) cc_final: 0.7443 (ppp) REVERT: E 99 ASN cc_start: 0.8822 (m-40) cc_final: 0.8411 (t0) REVERT: E 161 MET cc_start: 0.8655 (tpp) cc_final: 0.8443 (tpt) REVERT: E 195 ASN cc_start: 0.7765 (t0) cc_final: 0.7533 (t0) REVERT: E 356 ASN cc_start: 0.8281 (p0) cc_final: 0.8078 (p0) REVERT: E 368 ASP cc_start: 0.8526 (p0) cc_final: 0.8272 (p0) REVERT: E 452 LEU cc_start: 0.9442 (mp) cc_final: 0.9070 (tp) REVERT: F 536 THR cc_start: 0.8552 (p) cc_final: 0.8300 (t) REVERT: F 588 ARG cc_start: 0.8910 (tmm-80) cc_final: 0.8656 (tmm-80) REVERT: F 591 GLN cc_start: 0.9188 (tt0) cc_final: 0.8550 (tt0) REVERT: F 621 GLU cc_start: 0.8355 (pt0) cc_final: 0.7755 (pt0) REVERT: F 648 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8631 (tm-30) REVERT: F 657 GLU cc_start: 0.9000 (tp30) cc_final: 0.8693 (tp30) REVERT: A 53 PHE cc_start: 0.7954 (m-10) cc_final: 0.7385 (m-10) REVERT: A 125 LEU cc_start: 0.9469 (mp) cc_final: 0.9218 (mp) REVERT: A 161 MET cc_start: 0.9063 (tpp) cc_final: 0.8625 (tpp) REVERT: A 368 ASP cc_start: 0.8044 (p0) cc_final: 0.7335 (p0) REVERT: B 523 LEU cc_start: 0.9100 (mt) cc_final: 0.8832 (mt) REVERT: B 584 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8889 (tm-30) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1316 time to fit residues: 43.4412 Evaluate side-chains 174 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 0.0270 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 178 optimal weight: 40.0000 chunk 107 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN D 575 GLN E 170 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.063156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.049279 restraints weight = 73057.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050781 restraints weight = 42311.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.051814 restraints weight = 29605.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052511 restraints weight = 23194.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052880 restraints weight = 19702.852| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4821 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= 0.129 Angle : 0.631 15.833 22223 Z= 0.313 Chirality : 0.044 0.307 2800 Planarity : 0.003 0.042 2670 Dihedral : 4.500 29.785 2001 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 : 0.00 % 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: 0.16 (0.21), residues: 1659 helix: 0.25 (0.27), residues: 406 sheet: 0.49 (0.23), residues: 451 loop : -0.07 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.020 0.001 TYR C 217 PHE 0.014 0.001 PHE C 53 TRP 0.015 0.001 TRP F 631 HIS 0.008 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16073) covalent geometry : angle 0.59357 / 0.30 (21863) SS BOND : bond 0.00565 / 0.29 ( 33) SS BOND : angle 1.89153 / 1.08 ( 66) hydrogen bonds : bond 0.04196 / 2.69 ( 543) hydrogen bonds : angle 3.95827 / 2.74 ( 2262) link_ALPHA1-3 : bond 0.00414 / 0.21 ( 3) link_ALPHA1-3 : angle 1.48656 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00768 / 0.39 ( 3) link_ALPHA1-6 : angle 1.40265 / 0.98 ( 9) link_BETA1-4 : bond 0.00386 / 0.23 ( 28) link_BETA1-4 : angle 1.25381 / 0.87 ( 84) link_NAG-ASN : bond 0.00409 / 0.21 ( 64) link_NAG-ASN : angle 1.97318 / 1.35 ( 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 221 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.569 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: C 39 TYR cc_start: 0.8642 (m-80) cc_final: 0.7890 (m-80) REVERT: C 382 PHE cc_start: 0.8793 (m-80) cc_final: 0.8489 (m-80) REVERT: D 574 LYS cc_start: 0.9037 (pttp) cc_final: 0.8704 (pttp) REVERT: E 95 MET cc_start: 0.8882 (ptm) cc_final: 0.7501 (ppp) REVERT: E 99 ASN cc_start: 0.8913 (m-40) cc_final: 0.8431 (t0) REVERT: E 161 MET cc_start: 0.8727 (tpp) cc_final: 0.8500 (tpt) REVERT: E 195 ASN cc_start: 0.7725 (t0) cc_final: 0.7400 (t0) REVERT: E 368 ASP cc_start: 0.8637 (p0) cc_final: 0.8357 (p0) REVERT: E 452 LEU cc_start: 0.9461 (mp) cc_final: 0.9105 (tp) REVERT: F 535 MET cc_start: 0.8168 (mpp) cc_final: 0.7938 (mpp) REVERT: F 536 THR cc_start: 0.8577 (p) cc_final: 0.8337 (t) REVERT: F 588 ARG cc_start: 0.9007 (tmm-80) cc_final: 0.8740 (tmm-80) REVERT: F 591 GLN cc_start: 0.9193 (tt0) cc_final: 0.8594 (tt0) REVERT: F 621 GLU cc_start: 0.8416 (pt0) cc_final: 0.7839 (pt0) REVERT: A 125 LEU cc_start: 0.9500 (mp) cc_final: 0.9288 (mp) REVERT: A 161 MET cc_start: 0.9150 (tpp) cc_final: 0.8793 (tpp) REVERT: A 166 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7973 (mmt90) REVERT: A 211 GLU cc_start: 0.8486 (pm20) cc_final: 0.8220 (pm20) REVERT: A 368 ASP cc_start: 0.8406 (p0) cc_final: 0.7404 (p0) REVERT: A 425 ASN cc_start: 0.8865 (m110) cc_final: 0.8641 (m-40) REVERT: B 523 LEU cc_start: 0.9124 (mt) cc_final: 0.8859 (mt) REVERT: B 584 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8904 (tm-30) REVERT: B 654 GLU cc_start: 0.9030 (tp30) cc_final: 0.8088 (pt0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1286 time to fit residues: 42.6176 Evaluate side-chains 174 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN E 170 GLN E 183 GLN ** 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 585 HIS B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.048071 restraints weight = 75741.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049462 restraints weight = 45557.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050414 restraints weight = 32527.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051022 restraints weight = 26003.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051483 restraints weight = 22414.293| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16204 Z= 0.202 Angle : 0.687 16.185 22223 Z= 0.340 Chirality : 0.045 0.283 2800 Planarity : 0.004 0.046 2670 Dihedral : 4.681 30.576 2001 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.03 (0.21), residues: 1659 helix: 0.04 (0.26), residues: 417 sheet: 0.44 (0.23), residues: 460 loop : -0.11 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 298 TYR 0.041 0.002 TYR C 217 PHE 0.012 0.002 PHE C 53 TRP 0.024 0.002 TRP F 631 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (16073) covalent geometry : angle 0.65087 / 0.33 (21863) SS BOND : bond 0.00462 / 0.25 ( 33) SS BOND : angle 1.87726 / 1.08 ( 66) hydrogen bonds : bond 0.04419 / 2.86 ( 543) hydrogen bonds : angle 4.05747 / 2.80 ( 2262) link_ALPHA1-3 : bond 0.00345 / 0.18 ( 3) link_ALPHA1-3 : angle 1.64167 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00861 / 0.44 ( 3) link_ALPHA1-6 : angle 1.45391 / 1.00 ( 9) link_BETA1-4 : bond 0.00342 / 0.21 ( 28) link_BETA1-4 : angle 1.31166 / 0.92 ( 84) link_NAG-ASN : bond 0.00408 / 0.25 ( 64) link_NAG-ASN : angle 2.06728 / 1.43 ( 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 206 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8687 (m-80) cc_final: 0.7877 (m-80) REVERT: C 382 PHE cc_start: 0.8765 (m-80) cc_final: 0.8467 (m-80) REVERT: E 95 MET cc_start: 0.8910 (ptm) cc_final: 0.7588 (ppp) REVERT: E 99 ASN cc_start: 0.8813 (m-40) cc_final: 0.8484 (t0) REVERT: E 104 MET cc_start: 0.9144 (ttm) cc_final: 0.8905 (ttm) REVERT: E 161 MET cc_start: 0.8632 (tpp) cc_final: 0.8345 (tpt) REVERT: E 195 ASN cc_start: 0.7862 (t0) cc_final: 0.7477 (t0) REVERT: E 368 ASP cc_start: 0.8567 (p0) cc_final: 0.8290 (p0) REVERT: E 452 LEU cc_start: 0.9381 (mp) cc_final: 0.9126 (tp) REVERT: F 535 MET cc_start: 0.8147 (mpp) cc_final: 0.7911 (mpp) REVERT: F 588 ARG cc_start: 0.8909 (tmm-80) cc_final: 0.8686 (tmm-80) REVERT: F 591 GLN cc_start: 0.9235 (tt0) cc_final: 0.8656 (tt0) REVERT: F 599 SER cc_start: 0.9291 (p) cc_final: 0.8961 (m) REVERT: F 632 ASP cc_start: 0.8660 (p0) cc_final: 0.8455 (p0) REVERT: A 69 TRP cc_start: 0.8828 (m-90) cc_final: 0.8590 (m-90) REVERT: A 125 LEU cc_start: 0.9529 (mp) cc_final: 0.9286 (mp) REVERT: A 161 MET cc_start: 0.9105 (tpp) cc_final: 0.8705 (tpp) REVERT: B 584 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8905 (tm-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1320 time to fit residues: 40.6802 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 : 0.570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 181 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 129 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 170 GLN A 283 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.062214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.048739 restraints weight = 74757.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050148 restraints weight = 44983.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051098 restraints weight = 32123.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051700 restraints weight = 25672.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052154 restraints weight = 22148.320| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16204 Z= 0.150 Angle : 0.650 16.258 22223 Z= 0.324 Chirality : 0.045 0.270 2800 Planarity : 0.003 0.041 2670 Dihedral : 4.616 30.048 2001 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.00 (0.21), residues: 1659 helix: 0.06 (0.26), residues: 419 sheet: 0.41 (0.23), residues: 470 loop : -0.15 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 166 TYR 0.040 0.001 TYR C 217 PHE 0.014 0.001 PHE C 53 TRP 0.029 0.001 TRP B 631 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16073) covalent geometry : angle 0.61799 / 0.32 (21863) SS BOND : bond 0.00405 / 0.22 ( 33) SS BOND : angle 1.74559 / 1.00 ( 66) hydrogen bonds : bond 0.04204 / 2.72 ( 543) hydrogen bonds : angle 4.02008 / 2.78 ( 2262) link_ALPHA1-3 : bond 0.00270 / 0.14 ( 3) link_ALPHA1-3 : angle 1.50004 / 0.97 ( 9) link_ALPHA1-6 : bond 0.00851 / 0.43 ( 3) link_ALPHA1-6 : angle 1.44946 / 1.00 ( 9) link_BETA1-4 : bond 0.00353 / 0.21 ( 28) link_BETA1-4 : angle 1.25499 / 0.86 ( 84) link_NAG-ASN : bond 0.00544 / 0.26 ( 64) link_NAG-ASN : angle 1.86601 / 1.30 ( 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 207 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.625 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: 0.8707 (m-80) cc_final: 0.7928 (m-80) REVERT: C 382 PHE cc_start: 0.8668 (m-80) cc_final: 0.8424 (m-80) REVERT: D 574 LYS cc_start: 0.9128 (pttp) cc_final: 0.8610 (pttp) REVERT: E 95 MET cc_start: 0.8866 (ptm) cc_final: 0.7624 (ppp) REVERT: E 161 MET cc_start: 0.8558 (tpp) cc_final: 0.8202 (tpt) REVERT: E 195 ASN cc_start: 0.7789 (t0) cc_final: 0.7457 (t0) REVERT: E 368 ASP cc_start: 0.8560 (p0) cc_final: 0.8349 (p0) REVERT: E 452 LEU cc_start: 0.9328 (mp) cc_final: 0.9065 (tp) REVERT: F 588 ARG cc_start: 0.8893 (tmm-80) cc_final: 0.8628 (tmm-80) REVERT: F 591 GLN cc_start: 0.9182 (tt0) cc_final: 0.8566 (tt0) REVERT: F 599 SER cc_start: 0.9290 (p) cc_final: 0.9018 (m) REVERT: F 652 GLN cc_start: 0.8951 (mp10) cc_final: 0.8737 (pm20) REVERT: A 69 TRP cc_start: 0.8830 (m-90) cc_final: 0.8544 (m-90) REVERT: A 125 LEU cc_start: 0.9508 (mp) cc_final: 0.9280 (mp) REVERT: A 161 MET cc_start: 0.9061 (tpp) cc_final: 0.8675 (tpp) REVERT: A 443 ILE cc_start: 0.9182 (mm) cc_final: 0.8826 (tt) REVERT: B 584 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8907 (tm-30) REVERT: B 625 ASN cc_start: 0.8616 (m-40) cc_final: 0.8006 (m-40) REVERT: B 654 GLU cc_start: 0.9048 (tp30) cc_final: 0.8093 (pt0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1303 time to fit residues: 40.3564 Evaluate side-chains 156 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 173 optimal weight: 40.0000 chunk 85 optimal weight: 6.9990 chunk 148 optimal weight: 0.0770 chunk 84 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.0010 overall best weight: 3.0150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 575 GLN E 170 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.047753 restraints weight = 75791.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.049085 restraints weight = 45975.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.050030 restraints weight = 33246.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050648 restraints weight = 26660.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051040 restraints weight = 22978.983| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16204 Z= 0.211 Angle : 0.708 15.894 22223 Z= 0.350 Chirality : 0.047 0.274 2800 Planarity : 0.004 0.051 2670 Dihedral : 4.761 33.752 2001 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.16 (0.21), residues: 1659 helix: -0.14 (0.25), residues: 420 sheet: 0.30 (0.23), residues: 460 loop : -0.18 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.044 0.002 TYR C 217 PHE 0.011 0.002 PHE B 522 TRP 0.024 0.002 TRP B 631 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (16073) covalent geometry : angle 0.67414 / 0.34 (21863) SS BOND : bond 0.00441 / 0.24 ( 33) SS BOND : angle 1.76432 / 1.03 ( 66) hydrogen bonds : bond 0.04541 / 2.92 ( 543) hydrogen bonds : angle 4.11879 / 2.85 ( 2262) link_ALPHA1-3 : bond 0.00296 / 0.15 ( 3) link_ALPHA1-3 : angle 1.60644 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00661 / 0.34 ( 3) link_ALPHA1-6 : angle 1.39797 / 0.95 ( 9) link_BETA1-4 : bond 0.00331 / 0.20 ( 28) link_BETA1-4 : angle 1.29808 / 0.91 ( 84) link_NAG-ASN : bond 0.00578 / 0.30 ( 64) link_NAG-ASN : angle 2.07849 / 1.45 ( 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 201 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8790 (m-80) cc_final: 0.7924 (m-80) REVERT: C 382 PHE cc_start: 0.8697 (m-80) cc_final: 0.8464 (m-80) REVERT: C 484 TYR cc_start: 0.8467 (p90) cc_final: 0.8217 (p90) REVERT: D 574 LYS cc_start: 0.9097 (pttp) cc_final: 0.8761 (pttp) REVERT: E 95 MET cc_start: 0.8867 (ptm) cc_final: 0.7662 (ppp) REVERT: E 161 MET cc_start: 0.8603 (tpp) cc_final: 0.8274 (tpt) REVERT: E 195 ASN cc_start: 0.7861 (t0) cc_final: 0.7559 (t0) REVERT: E 368 ASP cc_start: 0.8589 (p0) cc_final: 0.8352 (p0) REVERT: E 452 LEU cc_start: 0.9347 (mp) cc_final: 0.9099 (tp) REVERT: F 588 ARG cc_start: 0.8884 (tmm-80) cc_final: 0.8671 (tmm-80) REVERT: F 591 GLN cc_start: 0.9170 (tt0) cc_final: 0.8540 (tt0) REVERT: F 652 GLN cc_start: 0.8908 (mp10) cc_final: 0.8534 (pm20) REVERT: F 655 LYS cc_start: 0.9525 (pptt) cc_final: 0.9319 (pptt) REVERT: A 125 LEU cc_start: 0.9537 (mp) cc_final: 0.9293 (mp) REVERT: A 161 MET cc_start: 0.9083 (tpp) cc_final: 0.8708 (tpp) REVERT: A 443 ILE cc_start: 0.9168 (mm) cc_final: 0.8872 (tt) REVERT: A 452 LEU cc_start: 0.9363 (mp) cc_final: 0.9152 (mp) REVERT: B 584 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8919 (tm-30) REVERT: B 625 ASN cc_start: 0.8111 (m-40) cc_final: 0.7904 (m-40) REVERT: B 654 GLU cc_start: 0.9129 (tp30) cc_final: 0.8837 (tp30) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1292 time to fit residues: 39.0895 Evaluate side-chains 151 residues out of total 1513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 575 GLN E 170 GLN A 283 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.048124 restraints weight = 75465.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049506 restraints weight = 45645.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050414 restraints weight = 32740.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051043 restraints weight = 26314.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051427 restraints weight = 22657.911| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16204 Z= 0.176 Angle : 0.687 15.889 22223 Z= 0.342 Chirality : 0.046 0.267 2800 Planarity : 0.004 0.041 2670 Dihedral : 4.730 33.938 2001 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -0.24 (0.21), residues: 1659 helix: -0.25 (0.25), residues: 419 sheet: 0.30 (0.23), residues: 456 loop : -0.24 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 298 TYR 0.023 0.001 TYR B 643 PHE 0.012 0.002 PHE C 53 TRP 0.028 0.002 TRP B 631 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (16073) covalent geometry : angle 0.65299 / 0.33 (21863) SS BOND : bond 0.00406 / 0.22 ( 33) SS BOND : angle 1.70902 / 0.99 ( 66) hydrogen bonds : bond 0.04481 / 2.89 ( 543) hydrogen bonds : angle 4.09613 / 2.82 ( 2262) link_ALPHA1-3 : bond 0.00370 / 0.19 ( 3) link_ALPHA1-3 : angle 1.58099 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00754 / 0.38 ( 3) link_ALPHA1-6 : angle 1.44261 / 0.99 ( 9) link_BETA1-4 : bond 0.00352 / 0.21 ( 28) link_BETA1-4 : angle 1.24070 / 0.86 ( 84) link_NAG-ASN : bond 0.00443 / 0.24 ( 64) link_NAG-ASN : angle 2.03206 / 1.41 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2299.64 seconds wall clock time: 40 minutes 56.73 seconds (2456.73 seconds total)