Starting phenix.real_space_refine on Mon Aug 25 08:14:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r9w_19014/08_2025/8r9w_19014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r9w_19014/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r9w_19014/08_2025/8r9w_19014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r9w_19014/08_2025/8r9w_19014.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r9w_19014/08_2025/8r9w_19014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r9w_19014/08_2025/8r9w_19014.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASP:plan': 3, 'TRP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASP:plan': 3, 'TRP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 6, 'TYR:plan': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'ASN:plan1': 3} 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: {'GLU:plan': 5, 'GLN:plan1': 7, 'ARG:plan': 8, 'ASP:plan': 3, 'TRP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 2} 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: 7.16, per 1000 atoms: 0.27 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.37 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: 7.31 Time building geometry restraints manager: 3.36 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: 0.07 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: 3.030 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: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.840 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.270 ------------------------------------------------------------------------------- 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 : 5.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 891 TYR 0.009 0.001 TYR C 222 PHE 0.011 0.001 PHE B 237 TRP 0.003 0.000 TRP C 973 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00350 (26730) covalent geometry : angle 0.57976 (36525) SS BOND : bond 0.00112 ( 36) SS BOND : angle 0.39948 ( 72) hydrogen bonds : bond 0.18625 ( 1132) hydrogen bonds : angle 7.92063 ( 3090) Misc. bond : bond 0.13200 ( 3) link_ALPHA1-3 : bond 0.00681 ( 3) link_ALPHA1-3 : angle 1.10785 ( 9) 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_NAG-ASN : bond 0.00161 ( 48) link_NAG-ASN : angle 1.39188 ( 144) *********************** 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 : 1.006 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: 0.1763 time to fit residues: 47.9940 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 : 0.997 ------------------------------------------------------------------------------- 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 879 GLN B 480 GLN B 879 GLN ** C 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 GLN C 879 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.056499 restraints weight = 87972.954| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.26 r_work: 0.2624 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 26844 Z= 0.161 Angle : 0.542 9.451 36822 Z= 0.283 Chirality : 0.044 0.223 4668 Planarity : 0.004 0.048 4662 Dihedral : 9.315 83.543 5324 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.58 % Allowed : 20.29 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.15), residues: 3507 helix: 2.65 (0.20), residues: 699 sheet: 0.08 (0.16), residues: 1047 loop : -0.75 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.010 0.001 TYR B 222 PHE 0.014 0.001 PHE B 377 TRP 0.005 0.001 TRP A 973 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00366 (26730) covalent geometry : angle 0.52803 (36525) SS BOND : bond 0.00160 ( 36) SS BOND : angle 0.62078 ( 72) hydrogen bonds : bond 0.04215 ( 1132) hydrogen bonds : angle 5.55984 ( 3090) Misc. bond : bond 0.00694 ( 3) link_ALPHA1-3 : bond 0.01276 ( 3) link_ALPHA1-3 : angle 2.63965 ( 9) link_ALPHA1-6 : bond 0.00311 ( 3) link_ALPHA1-6 : angle 2.43123 ( 9) link_BETA1-4 : bond 0.00367 ( 21) link_BETA1-4 : angle 1.74787 ( 63) link_NAG-ASN : bond 0.00235 ( 48) link_NAG-ASN : angle 1.44522 ( 144) *********************** 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 164 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 100 time to evaluate : 0.980 Fit side-chains REVERT: A 774 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7752 (t0) REVERT: B 90 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8270 (tpt) REVERT: B 135 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7191 (mt) REVERT: B 276 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8607 (pt0) REVERT: B 388 MET cc_start: 0.9415 (mtt) cc_final: 0.9048 (mtt) REVERT: B 774 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8174 (t0) REVERT: C 774 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8246 (t0) outliers start: 64 outliers final: 25 residues processed: 155 average time/residue: 0.1671 time to fit residues: 43.4770 Evaluate side-chains 128 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 685 VAL 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 B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 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 593 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 364 ASP 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 887 ILE Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 234 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 257 optimal weight: 0.1980 chunk 284 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 318 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 242 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.085702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057042 restraints weight = 91305.420| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.35 r_work: 0.2641 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 26844 Z= 0.102 Angle : 0.492 9.571 36822 Z= 0.255 Chirality : 0.043 0.236 4668 Planarity : 0.003 0.048 4662 Dihedral : 8.073 80.162 5314 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.38 % Allowed : 20.57 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.15), residues: 3507 helix: 2.76 (0.20), residues: 699 sheet: 0.17 (0.17), residues: 1014 loop : -0.66 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 669 TYR 0.014 0.001 TYR B 468 PHE 0.011 0.001 PHE B 919 TRP 0.003 0.000 TRP C 973 HIS 0.002 0.000 HIS A 421 Details of bonding type rmsd covalent geometry : bond 0.00227 (26730) covalent geometry : angle 0.48115 (36525) SS BOND : bond 0.00095 ( 36) SS BOND : angle 0.51401 ( 72) hydrogen bonds : bond 0.03568 ( 1132) hydrogen bonds : angle 5.02755 ( 3090) Misc. bond : bond 0.00282 ( 3) link_ALPHA1-3 : bond 0.01402 ( 3) link_ALPHA1-3 : angle 1.59274 ( 9) link_ALPHA1-6 : bond 0.00505 ( 3) link_ALPHA1-6 : angle 2.17358 ( 9) link_BETA1-4 : bond 0.00416 ( 21) link_BETA1-4 : angle 1.54779 ( 63) link_NAG-ASN : bond 0.00139 ( 48) link_NAG-ASN : angle 1.25877 ( 144) *********************** 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 163 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 104 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7826 (t0) REVERT: B 90 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8336 (tpt) REVERT: B 135 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6919 (mt) REVERT: B 272 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8519 (ptt90) REVERT: B 276 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8438 (pt0) REVERT: B 316 MET cc_start: 0.8334 (tpp) cc_final: 0.7859 (tpt) REVERT: B 774 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 272 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (ptt180) REVERT: C 774 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8162 (t0) outliers start: 59 outliers final: 30 residues processed: 158 average time/residue: 0.1756 time to fit residues: 45.4106 Evaluate side-chains 133 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 912 CYS Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 364 ASP 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 774 ASN Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 1000 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 8 optimal weight: 9.9990 chunk 190 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 134 optimal weight: 50.0000 chunk 217 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 144 optimal weight: 50.0000 chunk 10 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN B 589 GLN C 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.054641 restraints weight = 117861.883| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.77 r_work: 0.2567 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 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 = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26844 Z= 0.169 Angle : 0.523 9.641 36822 Z= 0.268 Chirality : 0.043 0.222 4668 Planarity : 0.003 0.042 4662 Dihedral : 7.557 78.144 5311 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.54 % Allowed : 20.45 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 693 sheet: 0.14 (0.17), residues: 996 loop : -0.67 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 669 TYR 0.011 0.001 TYR B 468 PHE 0.015 0.001 PHE B 377 TRP 0.006 0.001 TRP A 973 HIS 0.002 0.001 HIS C 933 Details of bonding type rmsd covalent geometry : bond 0.00394 (26730) covalent geometry : angle 0.50797 (36525) SS BOND : bond 0.00076 ( 36) SS BOND : angle 0.62020 ( 72) hydrogen bonds : bond 0.03813 ( 1132) hydrogen bonds : angle 4.90689 ( 3090) Misc. bond : bond 0.00652 ( 3) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 2.24383 ( 9) link_ALPHA1-6 : bond 0.00373 ( 3) link_ALPHA1-6 : angle 2.39223 ( 9) link_BETA1-4 : bond 0.00335 ( 21) link_BETA1-4 : angle 1.77451 ( 63) link_NAG-ASN : bond 0.00264 ( 48) link_NAG-ASN : angle 1.47607 ( 144) *********************** 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 163 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 100 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8751 (pt0) REVERT: A 774 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7755 (t0) REVERT: B 90 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8322 (tpt) REVERT: B 135 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7245 (mt) REVERT: B 276 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8646 (pm20) REVERT: B 348 MET cc_start: 0.8717 (mtm) cc_final: 0.8489 (mpp) REVERT: B 774 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8170 (t0) REVERT: C 379 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8818 (mp) REVERT: C 774 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8314 (t0) outliers start: 63 outliers final: 42 residues processed: 156 average time/residue: 0.1732 time to fit residues: 45.0397 Evaluate side-chains 140 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 92 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU 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 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 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL 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 711 SER Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1000 THR 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 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 887 ILE Chi-restraints excluded: chain C residue 912 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 246 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 174 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 54 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.055660 restraints weight = 101489.766| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.44 r_work: 0.2600 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 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 = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 26844 Z= 0.121 Angle : 0.491 9.617 36822 Z= 0.254 Chirality : 0.043 0.232 4668 Planarity : 0.003 0.045 4662 Dihedral : 7.202 75.723 5311 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.62 % Allowed : 20.61 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 696 sheet: 0.24 (0.17), residues: 987 loop : -0.66 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 290 TYR 0.011 0.001 TYR B 468 PHE 0.011 0.001 PHE C 839 TRP 0.005 0.000 TRP A 973 HIS 0.001 0.000 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00284 (26730) covalent geometry : angle 0.47899 (36525) SS BOND : bond 0.00091 ( 36) SS BOND : angle 0.56525 ( 72) hydrogen bonds : bond 0.03487 ( 1132) hydrogen bonds : angle 4.75362 ( 3090) Misc. bond : bond 0.00571 ( 3) link_ALPHA1-3 : bond 0.01230 ( 3) link_ALPHA1-3 : angle 2.00994 ( 9) link_ALPHA1-6 : bond 0.00501 ( 3) link_ALPHA1-6 : angle 2.28130 ( 9) link_BETA1-4 : bond 0.00374 ( 21) link_BETA1-4 : angle 1.55855 ( 63) link_NAG-ASN : bond 0.00148 ( 48) link_NAG-ASN : angle 1.30395 ( 144) *********************** 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 164 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 99 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7734 (t0) REVERT: A 823 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8657 (mt0) REVERT: B 90 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8314 (tpt) REVERT: B 120 MET cc_start: 0.9269 (tpt) cc_final: 0.9017 (mmm) REVERT: B 135 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6983 (mt) REVERT: B 276 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8614 (pm20) REVERT: B 348 MET cc_start: 0.8687 (mtm) cc_final: 0.8462 (mpp) REVERT: B 774 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8101 (t0) REVERT: B 823 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: C 379 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8782 (mp) REVERT: C 774 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8275 (t0) outliers start: 65 outliers final: 44 residues processed: 158 average time/residue: 0.1450 time to fit residues: 38.5459 Evaluate side-chains 147 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU 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 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 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 976 THR 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 230 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 528 THR 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 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 746 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 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 125 THR 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 593 VAL Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 653 ILE Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 718 MET 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 Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 10 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 108 optimal weight: 50.0000 chunk 109 optimal weight: 40.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.054333 restraints weight = 101191.260| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.48 r_work: 0.2563 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 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 = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26844 Z= 0.176 Angle : 0.523 9.660 36822 Z= 0.269 Chirality : 0.043 0.223 4668 Planarity : 0.003 0.044 4662 Dihedral : 7.283 76.642 5311 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.70 % Allowed : 20.85 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.15), residues: 3507 helix: 2.78 (0.20), residues: 693 sheet: 0.23 (0.17), residues: 993 loop : -0.70 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 669 TYR 0.011 0.001 TYR A 539 PHE 0.017 0.001 PHE B 377 TRP 0.007 0.001 TRP A 973 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00415 (26730) covalent geometry : angle 0.50784 (36525) SS BOND : bond 0.00100 ( 36) SS BOND : angle 0.66332 ( 72) hydrogen bonds : bond 0.03849 ( 1132) hydrogen bonds : angle 4.79336 ( 3090) Misc. bond : bond 0.00544 ( 3) link_ALPHA1-3 : bond 0.01086 ( 3) link_ALPHA1-3 : angle 2.28157 ( 9) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 2.26646 ( 9) link_BETA1-4 : bond 0.00335 ( 21) link_BETA1-4 : angle 1.78863 ( 63) link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 1.47574 ( 144) *********************** 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 166 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 99 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 823 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8685 (mt0) REVERT: B 90 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8245 (tpt) REVERT: B 120 MET cc_start: 0.9321 (tpt) cc_final: 0.9062 (mmm) REVERT: B 276 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8617 (pm20) REVERT: B 348 MET cc_start: 0.8738 (mtm) cc_final: 0.8500 (mpp) REVERT: B 774 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8057 (t0) REVERT: B 823 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8727 (mt0) REVERT: C 379 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8807 (mp) REVERT: C 774 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8299 (t0) REVERT: C 823 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8676 (mt0) outliers start: 67 outliers final: 42 residues processed: 161 average time/residue: 0.1671 time to fit residues: 45.1644 Evaluate side-chains 141 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 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 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 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 A residue 1000 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 528 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 664 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 746 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 B residue 1000 THR 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 364 ASP Chi-restraints excluded: chain C residue 379 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 823 GLN Chi-restraints excluded: chain C residue 887 ILE 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 213 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 311 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.054334 restraints weight = 101255.219| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.44 r_work: 0.2572 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 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 = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 26844 Z= 0.165 Angle : 0.515 9.665 36822 Z= 0.266 Chirality : 0.043 0.226 4668 Planarity : 0.004 0.047 4662 Dihedral : 7.066 72.923 5311 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.74 % Allowed : 20.81 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.15), residues: 3507 helix: 2.76 (0.20), residues: 693 sheet: 0.22 (0.17), residues: 978 loop : -0.71 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 290 TYR 0.012 0.001 TYR B 468 PHE 0.014 0.001 PHE A 839 TRP 0.006 0.001 TRP A 973 HIS 0.002 0.001 HIS C 933 Details of bonding type rmsd covalent geometry : bond 0.00392 (26730) covalent geometry : angle 0.50155 (36525) SS BOND : bond 0.00078 ( 36) SS BOND : angle 0.59099 ( 72) hydrogen bonds : bond 0.03740 ( 1132) hydrogen bonds : angle 4.76349 ( 3090) Misc. bond : bond 0.00699 ( 3) link_ALPHA1-3 : bond 0.01189 ( 3) link_ALPHA1-3 : angle 2.10546 ( 9) link_ALPHA1-6 : bond 0.00357 ( 3) link_ALPHA1-6 : angle 2.22731 ( 9) link_BETA1-4 : bond 0.00343 ( 21) link_BETA1-4 : angle 1.66423 ( 63) link_NAG-ASN : bond 0.00188 ( 48) link_NAG-ASN : angle 1.41417 ( 144) *********************** 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 164 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 96 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7765 (t0) REVERT: A 823 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8675 (mt0) REVERT: B 90 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8317 (tpt) REVERT: B 120 MET cc_start: 0.9331 (tpt) cc_final: 0.9082 (mmm) REVERT: B 135 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7306 (mt) REVERT: B 276 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8674 (pm20) REVERT: B 348 MET cc_start: 0.8776 (mtm) cc_final: 0.8560 (mpp) REVERT: B 388 MET cc_start: 0.9539 (mtm) cc_final: 0.9298 (mtt) REVERT: B 774 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8045 (t0) REVERT: B 823 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8658 (mt0) REVERT: C 379 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8844 (mp) REVERT: C 774 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8336 (t0) REVERT: C 823 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8669 (mt0) outliers start: 68 outliers final: 47 residues processed: 158 average time/residue: 0.1598 time to fit residues: 42.2752 Evaluate side-chains 148 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 92 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU 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 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 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 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 175 LEU Chi-restraints excluded: chain B residue 230 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 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 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 B residue 992 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 125 THR 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 711 SER Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 887 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 197 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 215 optimal weight: 0.9990 chunk 130 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 50.0000 chunk 287 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.083224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.054148 restraints weight = 109572.577| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.93 r_work: 0.2553 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 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 = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 26844 Z= 0.154 Angle : 0.515 11.414 36822 Z= 0.266 Chirality : 0.043 0.229 4668 Planarity : 0.004 0.056 4662 Dihedral : 6.878 71.210 5311 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.58 % Allowed : 21.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.15), residues: 3507 helix: 2.73 (0.20), residues: 693 sheet: 0.25 (0.17), residues: 978 loop : -0.71 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 669 TYR 0.010 0.001 TYR B 468 PHE 0.014 0.001 PHE C 839 TRP 0.005 0.001 TRP A 973 HIS 0.002 0.001 HIS C 933 Details of bonding type rmsd covalent geometry : bond 0.00370 (26730) covalent geometry : angle 0.50238 (36525) SS BOND : bond 0.00074 ( 36) SS BOND : angle 0.58148 ( 72) hydrogen bonds : bond 0.03683 ( 1132) hydrogen bonds : angle 4.74061 ( 3090) Misc. bond : bond 0.00891 ( 3) link_ALPHA1-3 : bond 0.01169 ( 3) link_ALPHA1-3 : angle 2.12624 ( 9) link_ALPHA1-6 : bond 0.00392 ( 3) link_ALPHA1-6 : angle 2.23648 ( 9) link_BETA1-4 : bond 0.00340 ( 21) link_BETA1-4 : angle 1.62924 ( 63) link_NAG-ASN : bond 0.00177 ( 48) link_NAG-ASN : angle 1.41299 ( 144) *********************** 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 164 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 100 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 823 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: B 58 LEU cc_start: 0.8510 (pt) cc_final: 0.8249 (pt) REVERT: B 90 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8284 (tpt) REVERT: B 120 MET cc_start: 0.9347 (tpt) cc_final: 0.8876 (tpp) REVERT: B 135 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7257 (mt) REVERT: B 276 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8720 (pm20) REVERT: B 348 MET cc_start: 0.8855 (mtm) cc_final: 0.8631 (mpp) REVERT: B 774 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8017 (t0) REVERT: B 823 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8640 (mt0) REVERT: C 379 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 774 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8327 (t0) REVERT: C 823 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8611 (mt0) outliers start: 64 outliers final: 47 residues processed: 160 average time/residue: 0.1595 time to fit residues: 42.3896 Evaluate side-chains 153 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU 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 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 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 A residue 1000 THR 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 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 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 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 B residue 992 ILE Chi-restraints excluded: chain B residue 1000 THR 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 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 711 SER Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 887 ILE 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 299 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 111 optimal weight: 50.0000 chunk 255 optimal weight: 0.0060 chunk 326 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.082489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.053513 restraints weight = 113784.636| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.77 r_work: 0.2534 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 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 = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 26844 Z= 0.198 Angle : 0.548 12.975 36822 Z= 0.283 Chirality : 0.044 0.223 4668 Planarity : 0.004 0.063 4662 Dihedral : 6.882 70.361 5311 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.74 % Allowed : 20.97 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.15), residues: 3507 helix: 2.68 (0.20), residues: 693 sheet: 0.25 (0.17), residues: 978 loop : -0.74 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 290 TYR 0.011 0.001 TYR A 539 PHE 0.017 0.001 PHE B 377 TRP 0.006 0.001 TRP C 973 HIS 0.002 0.001 HIS C 933 Details of bonding type rmsd covalent geometry : bond 0.00477 (26730) covalent geometry : angle 0.53412 (36525) SS BOND : bond 0.00100 ( 36) SS BOND : angle 0.67523 ( 72) hydrogen bonds : bond 0.03932 ( 1132) hydrogen bonds : angle 4.81842 ( 3090) Misc. bond : bond 0.01140 ( 3) link_ALPHA1-3 : bond 0.01099 ( 3) link_ALPHA1-3 : angle 2.15434 ( 9) link_ALPHA1-6 : bond 0.00327 ( 3) link_ALPHA1-6 : angle 2.28341 ( 9) link_BETA1-4 : bond 0.00335 ( 21) link_BETA1-4 : angle 1.75365 ( 63) link_NAG-ASN : bond 0.00258 ( 48) link_NAG-ASN : angle 1.51710 ( 144) *********************** 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 168 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 100 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9354 (mmm) cc_final: 0.8889 (mmm) REVERT: A 774 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7703 (t0) REVERT: A 823 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: B 58 LEU cc_start: 0.8646 (pt) cc_final: 0.8372 (pt) REVERT: B 90 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8234 (tpt) REVERT: B 120 MET cc_start: 0.9382 (tpt) cc_final: 0.8945 (tpp) REVERT: B 135 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (mt) REVERT: B 276 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8712 (pm20) REVERT: B 348 MET cc_start: 0.8840 (mtm) cc_final: 0.8615 (mpp) REVERT: B 774 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8056 (t0) REVERT: B 823 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (mt0) REVERT: C 379 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8826 (mp) REVERT: C 774 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8345 (t0) REVERT: C 823 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8648 (mt0) outliers start: 68 outliers final: 51 residues processed: 163 average time/residue: 0.1532 time to fit residues: 41.7187 Evaluate side-chains 157 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 97 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 175 LEU 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 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 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 A residue 1000 THR 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 175 LEU Chi-restraints excluded: chain B residue 230 LEU 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 664 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 746 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 992 ILE Chi-restraints excluded: chain B residue 1000 THR 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 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 528 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 711 SER Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 887 ILE 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 234 optimal weight: 1.9990 chunk 319 optimal weight: 0.4980 chunk 342 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 112 optimal weight: 40.0000 chunk 57 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 24 optimal weight: 0.0770 chunk 229 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.084410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.055511 restraints weight = 97691.605| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.67 r_work: 0.2600 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 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 = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 26844 Z= 0.102 Angle : 0.517 15.794 36822 Z= 0.269 Chirality : 0.042 0.246 4668 Planarity : 0.004 0.064 4662 Dihedral : 6.482 66.316 5311 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.25 % Allowed : 21.38 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.15), residues: 3507 helix: 2.73 (0.20), residues: 693 sheet: 0.24 (0.17), residues: 978 loop : -0.58 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 290 TYR 0.011 0.001 TYR C 222 PHE 0.010 0.001 PHE A 919 TRP 0.003 0.000 TRP A 973 HIS 0.001 0.000 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00259 (26730) covalent geometry : angle 0.50712 (36525) SS BOND : bond 0.00105 ( 36) SS BOND : angle 0.57405 ( 72) hydrogen bonds : bond 0.03237 ( 1132) hydrogen bonds : angle 4.63249 ( 3090) Misc. bond : bond 0.00953 ( 3) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 2.03684 ( 9) link_ALPHA1-6 : bond 0.00601 ( 3) link_ALPHA1-6 : angle 2.13222 ( 9) link_BETA1-4 : bond 0.00422 ( 21) link_BETA1-4 : angle 1.39985 ( 63) link_NAG-ASN : bond 0.00180 ( 48) link_NAG-ASN : angle 1.27202 ( 144) ********************** 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 163 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 1.014 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 120 MET cc_start: 0.9300 (mmm) cc_final: 0.8593 (mmm) REVERT: A 774 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.7779 (t0) REVERT: A 823 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: B 58 LEU cc_start: 0.8609 (pt) cc_final: 0.8366 (pt) REVERT: B 90 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8355 (tpt) REVERT: B 120 MET cc_start: 0.9356 (tpt) cc_final: 0.8900 (tpp) REVERT: B 135 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7153 (mt) REVERT: B 276 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8653 (pm20) REVERT: B 348 MET cc_start: 0.8842 (mtm) cc_final: 0.8595 (mpp) REVERT: B 774 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8064 (t0) REVERT: B 823 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: C 290 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6912 (mmm160) REVERT: C 379 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8766 (mp) REVERT: C 774 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8306 (t0) REVERT: C 823 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8448 (mt0) outliers start: 56 outliers final: 40 residues processed: 159 average time/residue: 0.1641 time to fit residues: 43.4319 Evaluate side-chains 153 residues out of total 3072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 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 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 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 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 450 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 664 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 746 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 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 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 634 SER 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 219 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 317 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 61 optimal weight: 0.8980 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 = 0.3392 r_free = 0.3392 target = 0.083982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.054942 restraints weight = 106920.120| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.74 r_work: 0.2582 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 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 = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 26844 Z= 0.118 Angle : 0.510 15.934 36822 Z= 0.263 Chirality : 0.042 0.240 4668 Planarity : 0.004 0.064 4662 Dihedral : 6.413 64.389 5311 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.17 % Allowed : 21.46 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.15), residues: 3507 helix: 2.75 (0.20), residues: 696 sheet: 0.35 (0.17), residues: 999 loop : -0.65 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 290 TYR 0.011 0.001 TYR B 468 PHE 0.012 0.001 PHE C 839 TRP 0.004 0.000 TRP A 973 HIS 0.001 0.000 HIS C 933 Details of bonding type rmsd covalent geometry : bond 0.00293 (26730) covalent geometry : angle 0.49808 (36525) SS BOND : bond 0.00141 ( 36) SS BOND : angle 0.64932 ( 72) hydrogen bonds : bond 0.03353 ( 1132) hydrogen bonds : angle 4.60375 ( 3090) Misc. bond : bond 0.00908 ( 3) link_ALPHA1-3 : bond 0.01201 ( 3) link_ALPHA1-3 : angle 2.08600 ( 9) link_ALPHA1-6 : bond 0.00525 ( 3) link_ALPHA1-6 : angle 2.18221 ( 9) link_BETA1-4 : bond 0.00365 ( 21) link_BETA1-4 : angle 1.49201 ( 63) link_NAG-ASN : bond 0.00139 ( 48) link_NAG-ASN : angle 1.34541 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7545.88 seconds wall clock time: 129 minutes 36.40 seconds (7776.40 seconds total)