Starting phenix.real_space_refine on Wed Jul 24 16:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r9w_19014/07_2024/8r9w_19014.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 16404 2.51 5 N 4437 2.21 5 O 5361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 636": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "C GLU 636": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26331 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "H" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "D" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "F" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "E" Number of atoms: 592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 121, 590 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 586 Chain: "G" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 517 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 185 Chain: "B" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 7330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7330 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 919} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.17, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA 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 " Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 5.4 seconds 7014 Ramachandran restraints generated. 3507 Oldfield, 0 Emsley, 3507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 66 sheets defined 23.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.791A pdb=" N LEU A 68 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 121 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A 122 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.499A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 618 through 641 removed outlier: 3.986A pdb=" N ILE A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 752 through 765 Processing helix chain 'A' and resid 774 through 795 Processing helix chain 'A' and resid 804 through 823 removed outlier: 3.651A pdb=" N ASN A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 845 through 853 Processing helix chain 'A' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE A1012 " --> pdb=" O ASN A1008 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.712A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.711A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.791A pdb=" N LEU B 68 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.650A pdb=" N MET B 120 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 121 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.499A pdb=" N ASN B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 371 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 603 Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 618 through 641 removed outlier: 3.986A pdb=" N ILE B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 651 Processing helix chain 'B' and resid 674 through 683 Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 774 through 795 Processing helix chain 'B' and resid 804 through 823 removed outlier: 3.651A pdb=" N ASN B 808 " --> pdb=" O SER B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 837 No H-bonds generated for 'chain 'B' and resid 835 through 837' Processing helix chain 'B' and resid 845 through 853 Processing helix chain 'B' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 865 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 955 No H-bonds generated for 'chain 'B' and resid 953 through 955' Processing helix chain 'B' and resid 987 through 989 No H-bonds generated for 'chain 'B' and resid 987 through 989' Processing helix chain 'B' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE B1012 " --> pdb=" O ASN B1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 69 removed outlier: 3.790A pdb=" N LEU C 68 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 removed outlier: 3.649A pdb=" N MET C 120 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 121 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 122 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.498A pdb=" N ASN C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 371 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 603 Processing helix chain 'C' and resid 605 through 613 Processing helix chain 'C' and resid 618 through 641 removed outlier: 3.987A pdb=" N ILE C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 651 Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 707 through 715 removed outlier: 3.622A pdb=" N ASN C 715 " --> pdb=" O SER C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 752 through 765 Processing helix chain 'C' and resid 774 through 795 Processing helix chain 'C' and resid 804 through 823 removed outlier: 3.650A pdb=" N ASN C 808 " --> pdb=" O SER C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 Processing helix chain 'C' and resid 835 through 837 No H-bonds generated for 'chain 'C' and resid 835 through 837' Processing helix chain 'C' and resid 845 through 853 Processing helix chain 'C' and resid 854 through 902 removed outlier: 3.771A pdb=" N ARG C 864 " --> pdb=" O GLN C 860 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 865 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 1008 through 1013 removed outlier: 3.695A pdb=" N ILE C1012 " --> pdb=" O ASN C1008 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY A 81 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 256 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 250 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 206 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.250A pdb=" N ILE A 141 " --> pdb=" O CYS A 157 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS A 157 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 181 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY A 499 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 493 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA9, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'A' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR A 478 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR A 468 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 460 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN A 945 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN A 968 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 966 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 577 through 587 removed outlier: 6.057A pdb=" N LEU A 936 " --> pdb=" O HIS A 917 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS A 917 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AB7, first strand: chain 'A' and resid 643 through 644 removed outlier: 6.214A pdb=" N THR A 643 " --> pdb=" O GLN B 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 994 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR H 111 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.919A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR D 111 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.346A pdb=" N LEU F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.664A pdb=" N TYR E 111 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.345A pdb=" N LEU G 11 " --> pdb=" O GLU G 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.767A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY B 81 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR B 250 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 206 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 101 through 105 removed outlier: 7.251A pdb=" N ILE B 141 " --> pdb=" O CYS B 157 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N CYS B 157 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 181 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY B 499 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE B 493 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AE5, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR B 350 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA B 314 " --> pdb=" O THR B 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER B 313 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 326 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B 311 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 328 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN B 309 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 306 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU B 344 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N VAL B 308 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B 346 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 310 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 333 through 335 Processing sheet with id=AE8, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AE9, first strand: chain 'B' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR B 478 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR B 468 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 460 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 537 through 539 Processing sheet with id=AF2, first strand: chain 'B' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN B 945 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN B 968 " --> pdb=" O ASN B 945 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 966 " --> pdb=" O SER B 947 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 577 through 587 removed outlier: 6.057A pdb=" N LEU B 936 " --> pdb=" O HIS B 917 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B 917 " --> pdb=" O LEU B 936 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 593 through 595 Processing sheet with id=AF5, first strand: chain 'B' and resid 643 through 644 removed outlier: 6.208A pdb=" N THR B 643 " --> pdb=" O GLN C 557 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'B' and resid 991 through 994 Processing sheet with id=AF7, first strand: chain 'C' and resid 80 through 88 removed outlier: 3.600A pdb=" N GLY C 81 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 256 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 250 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.618A pdb=" N GLN C 205 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE C 206 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 101 through 105 removed outlier: 7.250A pdb=" N ILE C 141 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS C 157 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS C 181 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 280 through 283 removed outlier: 3.548A pdb=" N GLY C 499 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 493 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AG3, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR C 350 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA C 314 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 320 through 328 removed outlier: 6.741A pdb=" N SER C 313 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 326 " --> pdb=" O ASN C 311 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C 311 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 328 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN C 309 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU C 306 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU C 344 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 308 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C 346 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 310 " --> pdb=" O ASN C 346 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AG6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AG7, first strand: chain 'C' and resid 433 through 434 removed outlier: 4.309A pdb=" N THR C 478 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR C 468 " --> pdb=" O VAL C 481 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE C 460 " --> pdb=" O TYR C 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 537 through 539 Processing sheet with id=AG9, first strand: chain 'C' and resid 569 through 574 removed outlier: 5.736A pdb=" N ASN C 945 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN C 968 " --> pdb=" O ASN C 945 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 966 " --> pdb=" O SER C 947 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 577 through 587 removed outlier: 6.056A pdb=" N LEU C 936 " --> pdb=" O HIS C 917 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS C 917 " --> pdb=" O LEU C 936 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 593 through 595 Processing sheet with id=AH3, first strand: chain 'C' and resid 991 through 994 1162 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.65 Time building geometry restraints manager: 11.36 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: 99.32 - 106.50: 550 106.50 - 113.69: 15600 113.69 - 120.87: 11258 120.87 - 128.05: 9020 128.05 - 135.23: 97 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: 9 1.94 - 2.68: 506 2.68 - 3.42: 34128 3.42 - 4.16: 60817 4.16 - 4.90: 112129 Nonbonded interactions: 207589 Sorted by model distance: nonbonded pdb=" O THR B 252 " pdb=" ND2 ASN C 456 " model vdw 1.198 2.520 nonbonded pdb=" O THR A 252 " pdb=" ND2 ASN B 456 " model vdw 1.209 2.520 nonbonded pdb=" ND2 ASN A 456 " pdb=" O THR C 252 " model vdw 1.232 2.520 nonbonded pdb=" NE2 GLN A 271 " pdb=" CB PRO A 285 " model vdw 1.298 3.520 nonbonded pdb=" NE2 GLN C 271 " pdb=" CB PRO C 285 " model vdw 1.298 3.520 ... (remaining 207584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 1 through 110 or resid 112 through 121)) selection = (chain 'E' and (resid 1 through 110 or resid 112 through 121)) selection = (chain 'H' and (resid 1 through 110 or resid 112 through 121)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'U' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 77.860 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.170 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.770 ------------------------------------------------------------------------------- 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 : 0.003 0.057 26730 Z= 0.229 Angle : 0.580 12.679 36525 Z= 0.292 Chirality : 0.044 0.262 4668 Planarity : 0.003 0.064 4662 Dihedral : 16.816 108.243 10185 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.72 % Allowed : 22.95 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3507 helix: 2.38 (0.20), residues: 696 sheet: 0.08 (0.16), residues: 1086 loop : -0.75 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 973 HIS 0.008 0.001 HIS B 275 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR C 222 ARG 0.001 0.000 ARG C 891 *********************** 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 fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 2.955 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: 0.4010 time to fit residues: 110.0668 Evaluate side-chains 110 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 606 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 468 TYR Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 922 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 142 optimal weight: 40.0000 chunk 275 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 chunk 167 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 318 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 589 GLN A 715 ASN A 879 GLN B 480 GLN B 589 GLN B 879 GLN C 480 GLN C 589 GLN C 879 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 26730 Z= 0.450 Angle : 0.597 9.525 36525 Z= 0.312 Chirality : 0.046 0.196 4668 Planarity : 0.004 0.050 4662 Dihedral : 9.220 83.354 5324 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.62 % Allowed : 19.81 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3507 helix: 2.67 (0.20), residues: 693 sheet: -0.06 (0.16), residues: 1017 loop : -0.83 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 973 HIS 0.005 0.001 HIS B 933 PHE 0.023 0.002 PHE B 377 TYR 0.015 0.001 TYR A 123 ARG 0.003 0.000 ARG C 560 *********************** 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 183 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 93 time to evaluate : 2.863 Fit side-chains revert: symmetry clash REVERT: B 90 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8209 (tpt) REVERT: B 276 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8647 (pt0) REVERT: B 348 MET cc_start: 0.8828 (mtm) cc_final: 0.8612 (mpp) REVERT: B 388 MET cc_start: 0.9474 (mtt) cc_final: 0.9198 (mtt) outliers start: 90 outliers final: 49 residues processed: 177 average time/residue: 0.3206 time to fit residues: 97.2006 Evaluate side-chains 144 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 94 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 450 SER 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 912 CYS Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 ASP 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 794 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 93 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 450 SER 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 922 THR Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Chi-restraints excluded: chain C residue 1000 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 319 optimal weight: 0.0980 chunk 344 optimal weight: 0.6980 chunk 284 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 108 optimal weight: 50.0000 chunk 256 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 C 847 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26730 Z= 0.127 Angle : 0.473 9.396 36525 Z= 0.247 Chirality : 0.042 0.230 4668 Planarity : 0.003 0.049 4662 Dihedral : 7.747 77.968 5314 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.97 % Allowed : 21.86 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3507 helix: 2.85 (0.20), residues: 699 sheet: 0.16 (0.17), residues: 999 loop : -0.72 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 973 HIS 0.001 0.000 HIS C 236 PHE 0.011 0.001 PHE B 919 TYR 0.011 0.001 TYR C 222 ARG 0.006 0.000 ARG A 292 *********************** 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 150 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 101 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.7948 (t0) REVERT: B 90 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8271 (tpt) REVERT: B 120 MET cc_start: 0.9278 (tpt) cc_final: 0.8756 (tpp) REVERT: B 135 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6938 (mt) REVERT: B 276 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8614 (pt0) REVERT: B 348 MET cc_start: 0.8808 (mtm) cc_final: 0.8575 (mpp) REVERT: B 388 MET cc_start: 0.9434 (mtt) cc_final: 0.9185 (mtt) REVERT: C 774 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8344 (t0) outliers start: 49 outliers final: 23 residues processed: 143 average time/residue: 0.3787 time to fit residues: 89.4541 Evaluate side-chains 122 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 554 SER 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 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 971 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 640 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 152 optimal weight: 50.0000 chunk 214 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 26730 Z= 0.233 Angle : 0.485 9.692 36525 Z= 0.253 Chirality : 0.043 0.231 4668 Planarity : 0.003 0.044 4662 Dihedral : 7.315 76.755 5311 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.93 % Allowed : 22.14 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3507 helix: 2.99 (0.20), residues: 693 sheet: 0.21 (0.17), residues: 1023 loop : -0.67 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 973 HIS 0.002 0.001 HIS C 414 PHE 0.014 0.001 PHE C 839 TYR 0.011 0.001 TYR B 468 ARG 0.004 0.000 ARG A 292 *********************** 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 144 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 823 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8677 (mt0) REVERT: B 90 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8259 (tpt) REVERT: B 120 MET cc_start: 0.9351 (tpt) cc_final: 0.8839 (tpp) REVERT: B 135 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7187 (mt) REVERT: B 348 MET cc_start: 0.8803 (mtm) cc_final: 0.8557 (mpp) REVERT: B 388 MET cc_start: 0.9464 (mtt) cc_final: 0.9230 (mtt) REVERT: C 379 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8797 (mp) outliers start: 48 outliers final: 32 residues processed: 139 average time/residue: 0.3523 time to fit residues: 81.9079 Evaluate side-chains 128 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 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 B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL 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 653 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 252 optimal weight: 0.0670 chunk 139 optimal weight: 50.0000 chunk 289 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26730 Z= 0.161 Angle : 0.464 9.592 36525 Z= 0.241 Chirality : 0.042 0.235 4668 Planarity : 0.003 0.045 4662 Dihedral : 6.841 73.052 5311 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.58 % Allowed : 21.98 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3507 helix: 2.92 (0.20), residues: 702 sheet: 0.27 (0.16), residues: 1059 loop : -0.67 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 973 HIS 0.002 0.000 HIS B 275 PHE 0.011 0.001 PHE C 839 TYR 0.010 0.001 TYR C 222 ARG 0.007 0.000 ARG C 290 *********************** 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 163 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 99 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9210 (mmm) cc_final: 0.8901 (tpt) REVERT: A 774 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7789 (t0) REVERT: A 823 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: B 135 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6981 (mt) REVERT: B 348 MET cc_start: 0.8877 (mtm) cc_final: 0.8623 (mpp) REVERT: B 388 MET cc_start: 0.9459 (mtt) cc_final: 0.9217 (mtt) REVERT: B 823 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: C 104 MET cc_start: 0.8500 (mtt) cc_final: 0.8232 (mtm) REVERT: C 823 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8500 (mt0) outliers start: 64 outliers final: 41 residues processed: 155 average time/residue: 0.3538 time to fit residues: 94.5999 Evaluate side-chains 144 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 98 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 421 HIS Chi-restraints excluded: chain A residue 451 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 554 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 684 VAL 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 125 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 50.0000 chunk 305 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 199 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 339 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 chunk 28 optimal weight: 0.2980 chunk 112 optimal weight: 50.0000 chunk 178 optimal weight: 6.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 847 GLN C 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26730 Z= 0.228 Angle : 0.483 9.703 36525 Z= 0.251 Chirality : 0.042 0.228 4668 Planarity : 0.003 0.042 4662 Dihedral : 6.758 70.750 5311 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.74 % Allowed : 22.22 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3507 helix: 3.14 (0.20), residues: 681 sheet: 0.27 (0.16), residues: 1044 loop : -0.64 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 973 HIS 0.003 0.001 HIS B 275 PHE 0.015 0.001 PHE B 377 TYR 0.012 0.001 TYR B 468 ARG 0.007 0.000 ARG B 669 *********************** 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 167 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 99 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7767 (t0) REVERT: A 823 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: B 90 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8252 (tpt) REVERT: B 135 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7253 (mt) REVERT: B 348 MET cc_start: 0.8874 (mtm) cc_final: 0.8634 (mpp) REVERT: B 388 MET cc_start: 0.9491 (mtt) cc_final: 0.9241 (mtt) REVERT: B 774 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8327 (t0) REVERT: B 823 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8615 (mt0) REVERT: C 120 MET cc_start: 0.9259 (mmm) cc_final: 0.9037 (tpt) REVERT: C 379 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 823 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8596 (mt0) outliers start: 68 outliers final: 46 residues processed: 160 average time/residue: 0.3156 time to fit residues: 86.2025 Evaluate side-chains 149 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 95 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 154 VAL 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 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 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 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 450 SER Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 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 289 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER 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 711 SER 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 Chi-restraints excluded: chain C residue 980 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 285 optimal weight: 0.8980 chunk 189 optimal weight: 0.0370 chunk 338 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 50.0000 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26730 Z= 0.134 Angle : 0.457 9.625 36525 Z= 0.237 Chirality : 0.042 0.238 4668 Planarity : 0.003 0.044 4662 Dihedral : 6.363 63.431 5311 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.46 % Allowed : 22.30 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3507 helix: 3.14 (0.20), residues: 684 sheet: 0.35 (0.16), residues: 1059 loop : -0.58 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 973 HIS 0.001 0.000 HIS C 236 PHE 0.010 0.001 PHE A 919 TYR 0.010 0.001 TYR C 222 ARG 0.006 0.000 ARG A 292 *********************** 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 160 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 99 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 823 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: B 58 LEU cc_start: 0.8516 (pt) cc_final: 0.8218 (pp) REVERT: B 90 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8251 (tpt) REVERT: B 120 MET cc_start: 0.9158 (tpp) cc_final: 0.8828 (tpp) REVERT: B 135 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6982 (mt) REVERT: B 348 MET cc_start: 0.8910 (mtm) cc_final: 0.8665 (mpp) REVERT: B 388 MET cc_start: 0.9468 (mtt) cc_final: 0.9223 (mtt) REVERT: B 774 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8349 (t0) REVERT: B 823 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: C 379 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8716 (mp) REVERT: C 774 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8412 (t0) REVERT: C 823 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8407 (mt0) outliers start: 61 outliers final: 46 residues processed: 152 average time/residue: 0.3450 time to fit residues: 88.3182 Evaluate side-chains 152 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 97 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 154 VAL 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 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 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 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 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 774 ASN Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 718 MET Chi-restraints excluded: chain C residue 774 ASN Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 912 CYS Chi-restraints excluded: chain C residue 959 SER Chi-restraints excluded: chain C residue 976 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 4.9990 chunk 135 optimal weight: 50.0000 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 265 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 847 GLN C 589 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 26730 Z= 0.274 Angle : 0.494 9.736 36525 Z= 0.256 Chirality : 0.043 0.231 4668 Planarity : 0.003 0.042 4662 Dihedral : 6.504 62.377 5311 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.62 % Allowed : 22.38 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3507 helix: 3.18 (0.20), residues: 675 sheet: 0.32 (0.17), residues: 1044 loop : -0.58 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 973 HIS 0.002 0.001 HIS B 414 PHE 0.016 0.001 PHE B 377 TYR 0.011 0.001 TYR A 539 ARG 0.007 0.000 ARG A 669 *********************** 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 161 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 96 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.7780 (t0) REVERT: A 823 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8638 (mt0) REVERT: B 90 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8146 (tpt) REVERT: B 135 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7272 (mt) REVERT: B 348 MET cc_start: 0.8883 (mtm) cc_final: 0.8663 (mpp) REVERT: B 388 MET cc_start: 0.9504 (mtt) cc_final: 0.9262 (mtt) REVERT: B 823 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8683 (mt0) REVERT: C 104 MET cc_start: 0.8353 (mtm) cc_final: 0.8027 (mtm) REVERT: C 379 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8805 (mp) REVERT: C 823 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8603 (mt0) outliers start: 65 outliers final: 52 residues processed: 155 average time/residue: 0.3373 time to fit residues: 88.2684 Evaluate side-chains 153 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 94 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER 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 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 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 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 823 GLN 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 289 VAL Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 502 THR Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 770 VAL 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 Chi-restraints excluded: chain C residue 980 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 0.5980 chunk 324 optimal weight: 3.9990 chunk 295 optimal weight: 0.1980 chunk 315 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 50.0000 chunk 247 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 chunk 284 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26730 Z= 0.142 Angle : 0.462 9.604 36525 Z= 0.239 Chirality : 0.042 0.239 4668 Planarity : 0.003 0.044 4662 Dihedral : 6.166 58.505 5311 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.33 % Allowed : 22.58 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3507 helix: 3.13 (0.20), residues: 684 sheet: 0.41 (0.16), residues: 1059 loop : -0.57 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 973 HIS 0.002 0.000 HIS A 421 PHE 0.010 0.001 PHE C 839 TYR 0.010 0.001 TYR C 222 ARG 0.012 0.000 ARG A 290 *********************** 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 155 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 97 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7847 (t0) REVERT: A 823 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: B 90 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8248 (tpt) REVERT: B 120 MET cc_start: 0.9096 (tpp) cc_final: 0.8721 (tpp) REVERT: B 135 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7200 (mt) REVERT: B 348 MET cc_start: 0.8904 (mtm) cc_final: 0.8666 (mpp) REVERT: B 388 MET cc_start: 0.9487 (mtt) cc_final: 0.9253 (mtt) REVERT: B 823 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: C 104 MET cc_start: 0.8386 (mtm) cc_final: 0.8063 (mtm) REVERT: C 379 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 823 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8435 (mt0) outliers start: 58 outliers final: 46 residues processed: 152 average time/residue: 0.3420 time to fit residues: 87.4114 Evaluate side-chains 150 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 97 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER 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 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain 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 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 823 GLN Chi-restraints excluded: chain B residue 912 CYS 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 289 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 711 SER 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 207 optimal weight: 4.9990 chunk 333 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 349 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 215 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26730 Z= 0.221 Angle : 0.477 9.703 36525 Z= 0.248 Chirality : 0.043 0.257 4668 Planarity : 0.003 0.052 4662 Dihedral : 6.203 58.235 5311 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.38 % Allowed : 22.46 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3507 helix: 3.11 (0.20), residues: 684 sheet: 0.40 (0.17), residues: 1044 loop : -0.59 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 973 HIS 0.002 0.000 HIS C 414 PHE 0.014 0.001 PHE C 839 TYR 0.010 0.001 TYR A 539 ARG 0.010 0.000 ARG A 290 ********************** 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 158 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 99 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7811 (t0) REVERT: A 823 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: B 90 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8198 (tpt) REVERT: B 120 MET cc_start: 0.9076 (tpp) cc_final: 0.8692 (tpp) REVERT: B 135 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7241 (mt) REVERT: B 348 MET cc_start: 0.8890 (mtm) cc_final: 0.8661 (mpp) REVERT: B 388 MET cc_start: 0.9499 (mtt) cc_final: 0.9248 (mtt) REVERT: B 733 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.9008 (m) REVERT: B 823 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: C 104 MET cc_start: 0.8402 (mtm) cc_final: 0.8078 (mtm) REVERT: C 379 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 823 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8579 (mt0) outliers start: 59 outliers final: 50 residues processed: 155 average time/residue: 0.3407 time to fit residues: 89.0618 Evaluate side-chains 154 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 96 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 468 TYR Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 634 SER 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 770 VAL Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 976 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 289 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 733 THR Chi-restraints excluded: chain B residue 794 SER Chi-restraints excluded: chain B residue 823 GLN 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 289 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 468 TYR Chi-restraints excluded: chain C residue 554 SER 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 711 SER Chi-restraints excluded: chain C residue 770 VAL 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 221 optimal weight: 3.9990 chunk 296 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 256 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 35 optimal weight: 0.0010 chunk 51 optimal weight: 0.4980 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.083281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.054507 restraints weight = 104466.923| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.67 r_work: 0.2565 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 153 | |-----------------------------------------------------------------------------| r_final: 0.2568 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26730 Z= 0.193 Angle : 0.475 13.404 36525 Z= 0.245 Chirality : 0.042 0.299 4668 Planarity : 0.003 0.053 4662 Dihedral : 5.946 56.744 5311 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.46 % Allowed : 22.38 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3507 helix: 3.08 (0.20), residues: 684 sheet: 0.41 (0.16), residues: 1065 loop : -0.57 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 973 HIS 0.001 0.000 HIS C 414 PHE 0.013 0.001 PHE C 839 TYR 0.011 0.001 TYR B 468 ARG 0.010 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.22 seconds wall clock time: 91 minutes 34.96 seconds (5494.96 seconds total)