Starting phenix.real_space_refine on Sun May 25 06:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.map" model { file = "/net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9w_19014/05_2025/8r9w_19014.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 129 5.16 5 C 16404 2.51 5 N 4437 2.21 5 O 5361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.89s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 26331 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "D" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "F" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "E" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "G" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.10, per 1000 atoms: 0.61 Number of scatterers: 26331 At special positions: 0 Unit cell: (184.982, 184.982, 152.278, 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 129 16.00 O 5361 8.00 N 4437 7.00 C 16404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 433 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 699 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 912 " distance=2.03 Simple disulfide: pdb=" SG CYS A 951 " - pdb=" SG CYS A 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 602 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 699 " - pdb=" SG CYS B 710 " distance=2.03 Simple disulfide: pdb=" SG CYS B 901 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 951 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 378 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 545 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 602 " - pdb=" SG CYS C 608 " distance=2.03 Simple disulfide: pdb=" SG CYS C 699 " - pdb=" SG CYS C 710 " distance=2.03 Simple disulfide: pdb=" SG CYS C 901 " - pdb=" SG CYS C 912 " distance=2.03 Simple disulfide: pdb=" SG CYS C 951 " - pdb=" SG CYS C 997 " distance=2.03 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=3, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1101 " - " ASN A 311 " " NAG A1102 " - " ASN A 652 " " NAG A1103 " - " ASN A 945 " " NAG A1104 " - " ASN A 494 " " NAG A1105 " - " ASN A 526 " " NAG A1106 " - " ASN A1003 " " NAG A1107 " - " ASN A 661 " " NAG A1108 " - " ASN A 162 " " NAG A1109 " - " ASN A 99 " " NAG A1110 " - " ASN A 184 " " NAG A1111 " - " ASN A 251 " " NAG B1101 " - " ASN B 311 " " NAG B1102 " - " ASN B 652 " " NAG B1103 " - " ASN B 945 " " NAG B1104 " - " ASN B 494 " " NAG B1105 " - " ASN B 526 " " NAG B1106 " - " ASN B1003 " " NAG B1107 " - " ASN B 661 " " NAG B1108 " - " ASN B 162 " " NAG B1109 " - " ASN B 99 " " NAG B1110 " - " ASN B 184 " " NAG B1111 " - " ASN B 251 " " NAG C1101 " - " ASN C 311 " " NAG C1102 " - " ASN C 652 " " NAG C1103 " - " ASN C 945 " " NAG C1104 " - " ASN C 494 " " NAG C1105 " - " ASN C 526 " " NAG C1106 " - " ASN C1003 " " NAG C1107 " - " ASN C 661 " " NAG C1108 " - " ASN C 162 " " NAG C1109 " - " ASN C 99 " " NAG C1110 " - " ASN C 184 " " NAG C1111 " - " ASN C 251 " " NAG I 1 " - " ASN A 788 " " NAG J 1 " - " ASN A 914 " " NAG K 1 " - " ASN A 472 " " NAG M 1 " - " ASN A 241 " " NAG N 1 " - " ASN A 74 " " NAG O 1 " - " ASN B 788 " " NAG P 1 " - " ASN B 914 " " NAG Q 1 " - " ASN B 472 " " NAG R 1 " - " ASN B 241 " " NAG S 1 " - " ASN B 74 " " NAG T 1 " - " ASN C 788 " " NAG U 1 " - " ASN C 914 " " NAG V 1 " - " ASN C 472 " " NAG W 1 " - " ASN C 241 " " NAG X 1 " - " ASN C 74 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 3.9 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 66 sheets defined 23.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.791A pdb=" N LEU A 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 121 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.499A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 641 removed outlier: 3.986A pdb=" N ILE A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 removed outlier: 3.651A pdb=" N ASN A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.712A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.791A pdb=" N LEU B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET B 120 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 121 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.499A pdb=" N ASN B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 371 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 618 through 641 removed outlier: 3.986A pdb=" N ILE B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 removed outlier: 3.651A pdb=" N ASN B 808 " --> pdb=" O SER B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 955 No H-bonds generated for 'chain 'B' and resid 953 through 955' Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.790A pdb=" N LEU C 68 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 removed outlier: 3.649A pdb=" N MET C 120 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 121 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 122 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.498A pdb=" N ASN C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 371 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 618 through 641 removed outlier: 3.987A pdb=" N ILE C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN C 715 " --> pdb=" O SER C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 removed outlier: 3.650A pdb=" N ASN C 808 " --> pdb=" O SER C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE C1012 " --> pdb=" O ASN C1008 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY A 81 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 256 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.250A pdb=" N ILE A 141 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS A 157 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 181 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'A' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR A 478 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN A 945 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN A 968 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 966 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 577 through 587 removed outlier: 6.057A pdb=" N LEU A 936 " --> pdb=" O HIS A 917 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS A 917 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB7, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.214A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR D 111 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR E 111 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.345A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY B 81 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR B 250 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 101 through 105 removed outlier: 7.251A pdb=" N ILE B 141 " --> pdb=" O CYS B 157 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS B 157 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 181 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AE5, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 306 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU B 344 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL B 308 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B 346 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 310 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AE8, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AE9, first strand: chain 'B' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR B 478 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AF2, first strand: chain 'B' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN B 945 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 968 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 966 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 577 through 587 removed outlier: 6.057A pdb=" N LEU B 936 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B 917 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 593 through 595 Processing sheet with id=AF5, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.208A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AF7, first strand: chain 'C' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY C 81 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 256 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 250 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 101 through 105 removed outlier: 7.250A pdb=" N ILE C 141 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS C 157 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS C 181 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AG3, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU C 306 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU C 344 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 308 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C 346 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 310 " --> pdb=" O ASN C 346 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AG6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AG7, first strand: chain 'C' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR C 478 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AG9, first strand: chain 'C' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN C 945 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN C 968 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 966 " --> pdb=" O SER C 947 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 577 through 587 removed outlier: 6.056A pdb=" N LEU C 936 " --> pdb=" O HIS C 917 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS C 917 " --> pdb=" O LEU C 936 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 593 through 595 Processing sheet with id=AH3, first strand: chain 'C' and resid 991 through 994 1162 hydrogen bonds defined for protein. 3090 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: 14.39 Time building geometry restraints manager: 7.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8677 1.34 - 1.46: 4354 1.46 - 1.57: 13519 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 26730 Sorted by residual: bond pdb=" N PRO C 907 " pdb=" CD PRO C 907 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N PRO B 907 " pdb=" CD PRO B 907 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO A 907 " pdb=" CD PRO A 907 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.19e-02 7.06e+03 7.07e+00 bond pdb=" N VAL B 277 " pdb=" CA VAL B 277 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.19e-02 7.06e+03 7.04e+00 ... (remaining 26725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 36211 2.54 - 5.07: 278 5.07 - 7.61: 27 7.61 - 10.14: 3 10.14 - 12.68: 6 Bond angle restraints: 36525 Sorted by residual: angle pdb=" CA PRO C 907 " pdb=" N PRO C 907 " pdb=" CD PRO C 907 " ideal model delta sigma weight residual 112.00 99.32 12.68 1.40e+00 5.10e-01 8.20e+01 angle pdb=" CA PRO A 907 " pdb=" N PRO A 907 " pdb=" CD PRO A 907 " ideal model delta sigma weight residual 112.00 99.36 12.64 1.40e+00 5.10e-01 8.15e+01 angle pdb=" CA PRO B 907 " pdb=" N PRO B 907 " pdb=" CD PRO B 907 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 angle pdb=" CA GLU A 278 " pdb=" C GLU A 278 " pdb=" O GLU A 278 " ideal model delta sigma weight residual 121.94 118.21 3.73 1.15e+00 7.56e-01 1.05e+01 angle pdb=" CA GLU C 278 " pdb=" C GLU C 278 " pdb=" O GLU C 278 " ideal model delta sigma weight residual 121.94 118.23 3.71 1.15e+00 7.56e-01 1.04e+01 ... (remaining 36520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 15423 21.65 - 43.30: 1206 43.30 - 64.95: 204 64.95 - 86.59: 78 86.59 - 108.24: 30 Dihedral angle restraints: 16941 sinusoidal: 6636 harmonic: 10305 Sorted by residual: dihedral pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" N PRO A 59 " pdb=" CA PRO A 59 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LEU B 58 " pdb=" C LEU B 58 " pdb=" N PRO B 59 " pdb=" CA PRO B 59 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LEU C 58 " pdb=" C LEU C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 16938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3797 0.052 - 0.105: 690 0.105 - 0.157: 160 0.157 - 0.209: 15 0.209 - 0.262: 6 Chirality restraints: 4668 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4665 not shown) Planarity restraints: 4710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 906 " -0.046 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO B 907 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 907 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 907 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 906 " -0.046 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO C 907 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 907 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 907 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 906 " -0.046 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 907 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 907 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 907 " -0.034 5.00e-02 4.00e+02 ... (remaining 4707 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 3 1.94 - 2.68: 500 2.68 - 3.42: 34128 3.42 - 4.16: 60817 4.16 - 4.90: 112129 Nonbonded interactions: 207577 Sorted by model distance: nonbonded pdb=" O THR B 252 " pdb=" ND2 ASN C 456 " model vdw 1.198 3.120 nonbonded pdb=" O THR A 252 " pdb=" ND2 ASN B 456 " model vdw 1.209 3.120 nonbonded pdb=" ND2 ASN A 456 " pdb=" O THR C 252 " model vdw 1.232 3.120 nonbonded pdb=" O CYS C 699 " pdb=" OH TYR C 714 " model vdw 2.164 3.040 nonbonded pdb=" O CYS A 699 " pdb=" OH TYR A 714 " model vdw 2.164 3.040 ... (remaining 207572 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 1 through 110 or resid 112 through 121)) selection = (chain 'E' and (resid 1 through 110 or resid 112 through 121)) selection = (chain 'H' and (resid 1 through 110 or resid 112 through 121)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'U' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 64.730 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.004 0.132 26844 Z= 0.231 Angle : 0.589 12.679 36822 Z= 0.293 Chirality : 0.044 0.262 4668 Planarity : 0.003 0.064 4662 Dihedral : 16.816 108.243 10185 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.72 % Allowed : 22.95 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3507 helix: 2.38 (0.20), residues: 696 sheet: 0.08 (0.16), residues: 1086 loop : -0.75 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 973 HIS 0.008 0.001 HIS B 275 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR C 222 ARG 0.001 0.000 ARG C 891 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 48) link_NAG-ASN : angle 1.39188 ( 144) link_ALPHA1-6 : bond 0.00466 ( 3) link_ALPHA1-6 : angle 1.61154 ( 9) link_BETA1-4 : bond 0.00407 ( 21) link_BETA1-4 : angle 1.70607 ( 63) link_ALPHA1-3 : bond 0.00681 ( 3) link_ALPHA1-3 : angle 1.10785 ( 9) hydrogen bonds : bond 0.18625 ( 1132) hydrogen bonds : angle 7.92063 ( 3090) SS BOND : bond 0.00112 ( 36) SS BOND : angle 0.39948 ( 72) covalent geometry : bond 0.00350 (26730) covalent geometry : angle 0.57976 (36525) Misc. bond : bond 0.13200 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 3.129 Fit side-chains REVERT: B 104 MET cc_start: 0.8502 (mtt) cc_final: 0.8267 (mtm) REVERT: B 375 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8803 (m) REVERT: B 468 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: B 669 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7449 (ttp-110) REVERT: C 375 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8943 (m) REVERT: C 969 PHE cc_start: 0.8191 (p90) cc_final: 0.7972 (p90) outliers start: 18 outliers final: 11 residues processed: 170 average time/residue: 0.3741 time to fit residues: 102.5696 Evaluate side-chains 110 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 922 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 167 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 318 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN A 589 GLN A 715 ASN A 879 GLN B 480 GLN B 589 GLN B 879 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN C 589 GLN C 879 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053792 restraints weight = 85195.030| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.19 r_work: 0.2560 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 26844 Z= 0.293 Angle : 0.630 9.538 36822 Z= 0.325 Chirality : 0.046 0.200 4668 Planarity : 0.004 0.049 4662 Dihedral : 9.344 84.158 5324 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.62 % Allowed : 19.20 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3507 helix: 2.56 (0.21), residues: 693 sheet: -0.04 (0.16), residues: 1047 loop : -0.86 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 973 HIS 0.005 0.001 HIS A 315 PHE 0.022 0.002 PHE C 839 TYR 0.013 0.001 TYR A 123 ARG 0.003 0.000 ARG B 560 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 48) link_NAG-ASN : angle 1.80543 ( 144) link_ALPHA1-6 : bond 0.00243 ( 3) link_ALPHA1-6 : angle 2.70851 ( 9) link_BETA1-4 : bond 0.00432 ( 21) link_BETA1-4 : angle 2.19676 ( 63) link_ALPHA1-3 : bond 0.00784 ( 3) link_ALPHA1-3 : angle 2.88173 ( 9) hydrogen bonds : bond 0.04831 ( 1132) hydrogen bonds : angle 5.57235 ( 3090) SS BOND : bond 0.00134 ( 36) SS BOND : angle 0.85023 ( 72) covalent geometry : bond 0.00683 (26730) covalent geometry : angle 0.61180 (36525) Misc. bond : bond 0.00531 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 98 time to evaluate : 2.773 Fit side-chains revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7772 (t0) REVERT: B 90 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8250 (tpt) REVERT: B 135 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7288 (mt) REVERT: B 276 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8630 (pt0) REVERT: B 388 MET cc_start: 0.9455 (mtt) cc_final: 0.9178 (mtt) REVERT: B 774 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8154 (t0) REVERT: C 774 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8371 (t0) outliers start: 90 outliers final: 40 residues processed: 178 average time/residue: 0.3216 time to fit residues: 97.1019 Evaluate side-chains 142 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Chi-restraints excluded: chain C residue 1000 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 125 optimal weight: 50.0000 chunk 39 optimal weight: 2.9990 chunk 133 optimal weight: 50.0000 chunk 146 optimal weight: 40.0000 chunk 32 optimal weight: 0.7980 chunk 262 optimal weight: 0.4980 chunk 296 optimal weight: 0.0040 chunk 259 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 346 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN C 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.056026 restraints weight = 103396.943| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.51 r_work: 0.2606 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 26844 Z= 0.098 Angle : 0.500 9.531 36822 Z= 0.260 Chirality : 0.043 0.233 4668 Planarity : 0.003 0.050 4662 Dihedral : 8.024 79.761 5314 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 21.05 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3507 helix: 2.75 (0.20), residues: 693 sheet: 0.15 (0.17), residues: 1011 loop : -0.70 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 973 HIS 0.001 0.000 HIS B 275 PHE 0.012 0.001 PHE B 919 TYR 0.012 0.001 TYR C 713 ARG 0.005 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 48) link_NAG-ASN : angle 1.26825 ( 144) link_ALPHA1-6 : bond 0.00466 ( 3) link_ALPHA1-6 : angle 2.16502 ( 9) link_BETA1-4 : bond 0.00427 ( 21) link_BETA1-4 : angle 1.52125 ( 63) link_ALPHA1-3 : bond 0.01406 ( 3) link_ALPHA1-3 : angle 1.76323 ( 9) hydrogen bonds : bond 0.03675 ( 1132) hydrogen bonds : angle 5.07399 ( 3090) SS BOND : bond 0.00098 ( 36) SS BOND : angle 0.53287 ( 72) covalent geometry : bond 0.00210 (26730) covalent geometry : angle 0.48878 (36525) Misc. bond : bond 0.00249 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7787 (t0) REVERT: B 90 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8307 (tpt) REVERT: B 120 MET cc_start: 0.9277 (tpt) cc_final: 0.8757 (tpp) REVERT: B 135 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7004 (mt) REVERT: B 276 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8723 (pm20) REVERT: B 348 MET cc_start: 0.8703 (mtm) cc_final: 0.8480 (mpp) REVERT: B 388 MET cc_start: 0.9428 (mtt) cc_final: 0.9176 (mtt) REVERT: B 774 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8106 (t0) REVERT: C 774 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8179 (t0) outliers start: 48 outliers final: 24 residues processed: 146 average time/residue: 0.3453 time to fit residues: 84.6580 Evaluate side-chains 123 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 316 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 50.0000 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN C 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.052889 restraints weight = 123692.740| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.88 r_work: 0.2521 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2525 r_free = 0.2525 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26844 Z= 0.237 Angle : 0.569 9.728 36822 Z= 0.291 Chirality : 0.045 0.219 4668 Planarity : 0.004 0.045 4662 Dihedral : 7.686 79.564 5311 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.09 % Allowed : 20.73 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3507 helix: 2.71 (0.20), residues: 693 sheet: 0.13 (0.17), residues: 990 loop : -0.80 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 973 HIS 0.002 0.001 HIS A 100 PHE 0.019 0.001 PHE C 839 TYR 0.012 0.001 TYR A 539 ARG 0.003 0.000 ARG C 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 48) link_NAG-ASN : angle 1.67389 ( 144) link_ALPHA1-6 : bond 0.00263 ( 3) link_ALPHA1-6 : angle 2.36294 ( 9) link_BETA1-4 : bond 0.00367 ( 21) link_BETA1-4 : angle 2.01002 ( 63) link_ALPHA1-3 : bond 0.01099 ( 3) link_ALPHA1-3 : angle 2.33164 ( 9) hydrogen bonds : bond 0.04309 ( 1132) hydrogen bonds : angle 5.07872 ( 3090) SS BOND : bond 0.00104 ( 36) SS BOND : angle 0.73394 ( 72) covalent geometry : bond 0.00557 (26730) covalent geometry : angle 0.55181 (36525) Misc. bond : bond 0.00305 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 97 time to evaluate : 3.011 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8746 (pt0) REVERT: A 774 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7712 (t0) REVERT: A 823 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8757 (mt0) REVERT: B 58 LEU cc_start: 0.8561 (pt) cc_final: 0.8307 (pt) REVERT: B 90 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8225 (tpt) REVERT: B 120 MET cc_start: 0.9354 (tpt) cc_final: 0.8865 (tpp) REVERT: B 276 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8654 (pm20) REVERT: B 388 MET cc_start: 0.9492 (mtt) cc_final: 0.9237 (mtt) REVERT: B 774 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8125 (t0) REVERT: B 932 MET cc_start: 0.9636 (mtp) cc_final: 0.9426 (mtp) REVERT: C 379 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8889 (mp) REVERT: C 774 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8332 (t0) outliers start: 52 outliers final: 36 residues processed: 144 average time/residue: 0.3438 time to fit residues: 83.5708 Evaluate side-chains 133 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 326 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 270 optimal weight: 0.7980 chunk 257 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.055579 restraints weight = 88188.632| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.25 r_work: 0.2603 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 26844 Z= 0.107 Angle : 0.494 9.614 36822 Z= 0.255 Chirality : 0.043 0.236 4668 Planarity : 0.003 0.047 4662 Dihedral : 7.074 75.432 5311 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.21 % Allowed : 21.18 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 693 sheet: 0.18 (0.17), residues: 1008 loop : -0.71 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 973 HIS 0.002 0.000 HIS C 236 PHE 0.011 0.001 PHE B 919 TYR 0.011 0.001 TYR B 468 ARG 0.007 0.000 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 48) link_NAG-ASN : angle 1.28454 ( 144) link_ALPHA1-6 : bond 0.00545 ( 3) link_ALPHA1-6 : angle 2.21817 ( 9) link_BETA1-4 : bond 0.00411 ( 21) link_BETA1-4 : angle 1.49267 ( 63) link_ALPHA1-3 : bond 0.01313 ( 3) link_ALPHA1-3 : angle 2.11736 ( 9) hydrogen bonds : bond 0.03471 ( 1132) hydrogen bonds : angle 4.78794 ( 3090) SS BOND : bond 0.00084 ( 36) SS BOND : angle 0.48497 ( 72) covalent geometry : bond 0.00252 (26730) covalent geometry : angle 0.48215 (36525) Misc. bond : bond 0.00215 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9232 (mmm) cc_final: 0.8922 (tpt) REVERT: A 276 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8655 (pm20) REVERT: A 774 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.7681 (t0) REVERT: A 823 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8613 (mt0) REVERT: B 58 LEU cc_start: 0.8569 (pt) cc_final: 0.8280 (pt) REVERT: B 120 MET cc_start: 0.9379 (tpt) cc_final: 0.8875 (tpp) REVERT: B 135 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7016 (mt) REVERT: B 276 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8571 (pm20) REVERT: B 388 MET cc_start: 0.9454 (mtt) cc_final: 0.9209 (mtt) REVERT: B 774 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8061 (t0) REVERT: B 823 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: C 272 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8498 (ptt90) REVERT: C 379 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8712 (mp) REVERT: C 774 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8261 (t0) REVERT: C 823 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (mt0) outliers start: 55 outliers final: 31 residues processed: 148 average time/residue: 0.3633 time to fit residues: 89.5412 Evaluate side-chains 135 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 204 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053567 restraints weight = 101533.253| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.49 r_work: 0.2549 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 26844 Z= 0.190 Angle : 0.532 9.692 36822 Z= 0.273 Chirality : 0.044 0.222 4668 Planarity : 0.004 0.042 4662 Dihedral : 7.099 75.283 5311 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.21 % Allowed : 21.54 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3507 helix: 2.76 (0.20), residues: 693 sheet: 0.17 (0.17), residues: 978 loop : -0.75 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 973 HIS 0.002 0.001 HIS B 414 PHE 0.017 0.001 PHE B 377 TYR 0.012 0.001 TYR A 539 ARG 0.005 0.000 ARG C 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 48) link_NAG-ASN : angle 1.56566 ( 144) link_ALPHA1-6 : bond 0.00325 ( 3) link_ALPHA1-6 : angle 2.30237 ( 9) link_BETA1-4 : bond 0.00343 ( 21) link_BETA1-4 : angle 1.81191 ( 63) link_ALPHA1-3 : bond 0.01157 ( 3) link_ALPHA1-3 : angle 2.24897 ( 9) hydrogen bonds : bond 0.03962 ( 1132) hydrogen bonds : angle 4.86442 ( 3090) SS BOND : bond 0.00093 ( 36) SS BOND : angle 0.66211 ( 72) covalent geometry : bond 0.00448 (26730) covalent geometry : angle 0.51671 (36525) Misc. bond : bond 0.00743 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 96 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9293 (mmm) cc_final: 0.8982 (tpt) REVERT: A 276 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8691 (pm20) REVERT: A 774 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7739 (t0) REVERT: A 823 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8701 (mt0) REVERT: B 58 LEU cc_start: 0.8676 (pt) cc_final: 0.8400 (pt) REVERT: B 90 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8265 (tpt) REVERT: B 135 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7348 (mt) REVERT: B 276 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8628 (pm20) REVERT: B 388 MET cc_start: 0.9488 (mtt) cc_final: 0.9230 (mtt) REVERT: B 774 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8133 (t0) REVERT: B 823 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8723 (mt0) REVERT: C 379 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8852 (mp) REVERT: C 774 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8367 (t0) REVERT: C 823 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (mt0) outliers start: 55 outliers final: 39 residues processed: 146 average time/residue: 0.3470 time to fit residues: 84.5705 Evaluate side-chains 139 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 91 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 502 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 116 optimal weight: 40.0000 chunk 277 optimal weight: 0.9980 chunk 134 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054850 restraints weight = 105236.787| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 3.55 r_work: 0.2577 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 26844 Z= 0.116 Angle : 0.498 9.672 36822 Z= 0.258 Chirality : 0.043 0.236 4668 Planarity : 0.004 0.046 4662 Dihedral : 6.751 70.120 5311 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.09 % Allowed : 21.70 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3507 helix: 2.79 (0.20), residues: 693 sheet: 0.18 (0.17), residues: 999 loop : -0.71 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 973 HIS 0.002 0.000 HIS C 236 PHE 0.012 0.001 PHE C 839 TYR 0.011 0.001 TYR B 468 ARG 0.007 0.000 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 48) link_NAG-ASN : angle 1.33452 ( 144) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 2.21762 ( 9) link_BETA1-4 : bond 0.00383 ( 21) link_BETA1-4 : angle 1.51024 ( 63) link_ALPHA1-3 : bond 0.01256 ( 3) link_ALPHA1-3 : angle 2.23058 ( 9) hydrogen bonds : bond 0.03513 ( 1132) hydrogen bonds : angle 4.72735 ( 3090) SS BOND : bond 0.00091 ( 36) SS BOND : angle 0.49840 ( 72) covalent geometry : bond 0.00282 (26730) covalent geometry : angle 0.48598 (36525) Misc. bond : bond 0.00718 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7790 (t0) REVERT: A 823 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8640 (mt0) REVERT: B 58 LEU cc_start: 0.8634 (pt) cc_final: 0.8428 (pt) REVERT: B 120 MET cc_start: 0.9198 (tpp) cc_final: 0.8860 (tpp) REVERT: B 135 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7178 (mt) REVERT: B 276 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8634 (pm20) REVERT: B 388 MET cc_start: 0.9477 (mtt) cc_final: 0.9229 (mtt) REVERT: B 774 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8107 (t0) REVERT: B 823 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: C 379 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 774 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8328 (t0) REVERT: C 823 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8589 (mt0) outliers start: 52 outliers final: 37 residues processed: 147 average time/residue: 0.3552 time to fit residues: 86.2683 Evaluate side-chains 142 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 347 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054493 restraints weight = 107240.052| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.73 r_work: 0.2565 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 26844 Z= 0.134 Angle : 0.505 10.609 36822 Z= 0.261 Chirality : 0.043 0.234 4668 Planarity : 0.004 0.054 4662 Dihedral : 6.618 67.077 5311 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.38 % Allowed : 21.42 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 693 sheet: 0.22 (0.17), residues: 978 loop : -0.70 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 973 HIS 0.001 0.000 HIS C 414 PHE 0.014 0.001 PHE C 839 TYR 0.009 0.001 TYR C 222 ARG 0.011 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 48) link_NAG-ASN : angle 1.38755 ( 144) link_ALPHA1-6 : bond 0.00527 ( 3) link_ALPHA1-6 : angle 2.29335 ( 9) link_BETA1-4 : bond 0.00362 ( 21) link_BETA1-4 : angle 1.55479 ( 63) link_ALPHA1-3 : bond 0.01203 ( 3) link_ALPHA1-3 : angle 2.23406 ( 9) hydrogen bonds : bond 0.03539 ( 1132) hydrogen bonds : angle 4.70604 ( 3090) SS BOND : bond 0.00081 ( 36) SS BOND : angle 0.53106 ( 72) covalent geometry : bond 0.00330 (26730) covalent geometry : angle 0.49251 (36525) Misc. bond : bond 0.00841 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 101 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.7742 (t0) REVERT: A 823 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8598 (mt0) REVERT: B 58 LEU cc_start: 0.8680 (pt) cc_final: 0.8430 (pt) REVERT: B 90 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8298 (tpt) REVERT: B 120 MET cc_start: 0.9197 (tpp) cc_final: 0.8813 (tpp) REVERT: B 135 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7230 (mt) REVERT: B 276 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8647 (pm20) REVERT: B 388 MET cc_start: 0.9495 (mtt) cc_final: 0.9247 (mtt) REVERT: B 774 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8057 (t0) REVERT: B 823 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: C 379 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8827 (mp) REVERT: C 774 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8329 (t0) REVERT: C 823 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8472 (mt0) outliers start: 59 outliers final: 44 residues processed: 155 average time/residue: 0.3579 time to fit residues: 93.4154 Evaluate side-chains 148 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 95 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 219 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 155 optimal weight: 40.0000 chunk 339 optimal weight: 2.9990 chunk 114 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.083669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.054658 restraints weight = 115012.707| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.89 r_work: 0.2564 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 26844 Z= 0.126 Angle : 0.508 12.338 36822 Z= 0.263 Chirality : 0.043 0.236 4668 Planarity : 0.004 0.062 4662 Dihedral : 6.473 64.255 5311 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.38 % Allowed : 21.30 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3507 helix: 2.75 (0.20), residues: 693 sheet: 0.14 (0.17), residues: 969 loop : -0.62 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 973 HIS 0.001 0.000 HIS C 414 PHE 0.012 0.001 PHE C 839 TYR 0.010 0.001 TYR C 539 ARG 0.008 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 48) link_NAG-ASN : angle 1.33397 ( 144) link_ALPHA1-6 : bond 0.00551 ( 3) link_ALPHA1-6 : angle 2.27425 ( 9) link_BETA1-4 : bond 0.00377 ( 21) link_BETA1-4 : angle 1.49163 ( 63) link_ALPHA1-3 : bond 0.01210 ( 3) link_ALPHA1-3 : angle 2.23827 ( 9) hydrogen bonds : bond 0.03470 ( 1132) hydrogen bonds : angle 4.66952 ( 3090) SS BOND : bond 0.00094 ( 36) SS BOND : angle 0.54068 ( 72) covalent geometry : bond 0.00315 (26730) covalent geometry : angle 0.49623 (36525) Misc. bond : bond 0.01102 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 102 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7761 (t0) REVERT: A 823 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8581 (mt0) REVERT: B 58 LEU cc_start: 0.8667 (pt) cc_final: 0.8421 (pt) REVERT: B 90 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8306 (tpt) REVERT: B 120 MET cc_start: 0.9144 (tpp) cc_final: 0.8765 (tpp) REVERT: B 135 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7178 (mt) REVERT: B 276 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8647 (pm20) REVERT: B 388 MET cc_start: 0.9496 (mtt) cc_final: 0.9263 (mtt) REVERT: B 733 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8955 (m) REVERT: B 774 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 823 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: C 379 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8796 (mp) REVERT: C 774 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8332 (t0) REVERT: C 823 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8436 (mt0) outliers start: 59 outliers final: 45 residues processed: 158 average time/residue: 0.3378 time to fit residues: 89.7192 Evaluate side-chains 152 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 338 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 245 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.055097 restraints weight = 80832.664| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.27 r_work: 0.2596 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 26844 Z= 0.136 Angle : 0.522 15.879 36822 Z= 0.271 Chirality : 0.043 0.237 4668 Planarity : 0.004 0.064 4662 Dihedral : 6.399 62.054 5311 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.38 % Allowed : 21.46 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3507 helix: 2.77 (0.21), residues: 693 sheet: 0.18 (0.17), residues: 948 loop : -0.63 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 973 HIS 0.002 0.000 HIS A 315 PHE 0.013 0.001 PHE C 839 TYR 0.012 0.001 TYR B 468 ARG 0.009 0.000 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 48) link_NAG-ASN : angle 1.37107 ( 144) link_ALPHA1-6 : bond 0.00558 ( 3) link_ALPHA1-6 : angle 2.31000 ( 9) link_BETA1-4 : bond 0.00369 ( 21) link_BETA1-4 : angle 1.52656 ( 63) link_ALPHA1-3 : bond 0.01159 ( 3) link_ALPHA1-3 : angle 2.23633 ( 9) hydrogen bonds : bond 0.03482 ( 1132) hydrogen bonds : angle 4.67034 ( 3090) SS BOND : bond 0.00081 ( 36) SS BOND : angle 0.58437 ( 72) covalent geometry : bond 0.00340 (26730) covalent geometry : angle 0.50949 (36525) Misc. bond : bond 0.00989 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 102 time to evaluate : 2.893 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: A 774 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 823 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: B 58 LEU cc_start: 0.8677 (pt) cc_final: 0.8439 (pt) REVERT: B 90 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8289 (tpt) REVERT: B 120 MET cc_start: 0.9119 (tpp) cc_final: 0.8732 (tpp) REVERT: B 135 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7224 (mt) REVERT: B 276 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8633 (pm20) REVERT: B 388 MET cc_start: 0.9482 (mtt) cc_final: 0.9216 (mtt) REVERT: B 733 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9001 (m) REVERT: B 774 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 823 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: C 379 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 774 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8347 (t0) REVERT: C 823 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8460 (mt0) outliers start: 59 outliers final: 48 residues processed: 158 average time/residue: 0.3539 time to fit residues: 93.7144 Evaluate side-chains 155 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 6 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 140 optimal weight: 0.0020 chunk 132 optimal weight: 50.0000 chunk 237 optimal weight: 0.8980 chunk 350 optimal weight: 0.9990 chunk 325 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 767 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.084507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.055666 restraints weight = 111927.228| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.98 r_work: 0.2593 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.155 26844 Z= 0.098 Angle : 0.492 15.579 36822 Z= 0.254 Chirality : 0.042 0.251 4668 Planarity : 0.004 0.062 4662 Dihedral : 6.126 58.353 5311 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.09 % Allowed : 21.78 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 696 sheet: 0.39 (0.17), residues: 993 loop : -0.64 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 973 HIS 0.001 0.000 HIS C 140 PHE 0.011 0.001 PHE A 919 TYR 0.011 0.001 TYR B 468 ARG 0.012 0.000 ARG C 290 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 48) link_NAG-ASN : angle 1.23760 ( 144) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 2.22526 ( 9) link_BETA1-4 : bond 0.00417 ( 21) link_BETA1-4 : angle 1.33988 ( 63) link_ALPHA1-3 : bond 0.01171 ( 3) link_ALPHA1-3 : angle 2.14468 ( 9) hydrogen bonds : bond 0.03213 ( 1132) hydrogen bonds : angle 4.55016 ( 3090) SS BOND : bond 0.00147 ( 36) SS BOND : angle 0.53359 ( 72) covalent geometry : bond 0.00235 (26730) covalent geometry : angle 0.48126 (36525) Misc. bond : bond 0.00980 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14448.56 seconds wall clock time: 251 minutes 32.42 seconds (15092.42 seconds total)