Starting phenix.real_space_refine on Wed Mar 20 08:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z85_14543/03_2024/7z85_14543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z85_14543/03_2024/7z85_14543.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/7z85_14543/03_2024/7z85_14543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z85_14543/03_2024/7z85_14543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z85_14543/03_2024/7z85_14543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z85_14543/03_2024/7z85_14543.pdb" } 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= 0.005 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 123 5.16 5 C 17084 2.51 5 N 4396 2.21 5 O 5231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26834 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 Chain: "D" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 Chain: "E" Number of atoms: 976 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} bond proxies already assigned to first conformer: 985 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.92, per 1000 atoms: 0.56 Number of scatterers: 26834 At special positions: 0 Unit cell: (127.2, 136.74, 215.18, 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 123 16.00 O 5231 8.00 N 4396 7.00 C 17084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG ACYS F 22 " - pdb=" SG ACYS F 96 " distance=2.04 Simple disulfide: pdb=" SG BCYS F 22 " - pdb=" SG BCYS F 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS D 22 " - pdb=" SG ACYS D 96 " distance=2.03 Simple disulfide: pdb=" SG BCYS D 22 " - pdb=" SG BCYS D 96 " distance=2.03 Simple disulfide: pdb=" SG ACYS E 22 " - pdb=" SG ACYS E 96 " distance=2.03 Simple disulfide: pdb=" SG BCYS E 22 " - pdb=" SG BCYS E 96 " distance=2.04 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 10.04 Conformation dependent library (CDL) restraints added in 5.2 seconds 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6248 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 53 sheets defined 25.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.801A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.501A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.357A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.879A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.973A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.693A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.730A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.317A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.943A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.787A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.666A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.772A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.726A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.681A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.249A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.951A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.632A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.334A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.721A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.066A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.591A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.744A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.261A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.026A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.809A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.146A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.726A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.565A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.795A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.871A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.805A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.251A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.702A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.332A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.568A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.851A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.207A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.811A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.660A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.107A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.807A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.811A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.303A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.690A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.403A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.636A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.967A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.508A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.787A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.148A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.533A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.694A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.836A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.800A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.215A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.447A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.714A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.872A pdb=" N ALA F 33 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.856A pdb=" N TYR F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.556A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.542A pdb=" N ALA D 33 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.738A pdb=" N VAL E 5 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.380A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA E 33 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.380A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) 1173 hydrogen bonds defined for protein. 3153 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: 11.96 Time building geometry restraints manager: 11.02 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: 8453 1.34 - 1.46: 6979 1.46 - 1.59: 11837 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 27425 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG C1408 " pdb=" O5 NAG C1408 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.355 0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" C1 NAG P 1 " pdb=" C2 NAG P 1 " ideal model delta sigma weight residual 1.532 1.481 0.051 2.00e-02 2.50e+03 6.40e+00 ... (remaining 27420 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.36: 533 105.36 - 112.53: 14478 112.53 - 119.69: 8327 119.69 - 126.86: 13711 126.86 - 134.03: 270 Bond angle restraints: 37319 Sorted by residual: angle pdb=" C SER F 25 " pdb=" N GLY F 26 " pdb=" CA GLY F 26 " ideal model delta sigma weight residual 121.86 128.50 -6.64 8.50e-01 1.38e+00 6.11e+01 angle pdb=" C SER D 25 " pdb=" N GLY D 26 " pdb=" CA GLY D 26 " ideal model delta sigma weight residual 121.86 125.64 -3.78 8.50e-01 1.38e+00 1.98e+01 angle pdb=" CA LEU C 110 " pdb=" CB LEU C 110 " pdb=" CG LEU C 110 " ideal model delta sigma weight residual 116.30 128.75 -12.45 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 120.19 -6.29 1.80e+00 3.09e-01 1.22e+01 angle pdb=" N SER F 25 " pdb=" CA SER F 25 " pdb=" C SER F 25 " ideal model delta sigma weight residual 109.41 114.70 -5.29 1.52e+00 4.33e-01 1.21e+01 ... (remaining 37314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 15688 17.24 - 34.48: 1100 34.48 - 51.72: 278 51.72 - 68.96: 47 68.96 - 86.19: 29 Dihedral angle restraints: 17142 sinusoidal: 7409 harmonic: 9733 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 175.20 -82.20 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -160.82 74.82 1 1.00e+01 1.00e-02 7.09e+01 ... (remaining 17139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3583 0.067 - 0.134: 774 0.134 - 0.202: 62 0.202 - 0.269: 10 0.269 - 0.336: 2 Chirality restraints: 4431 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU B 916 " pdb=" CB LEU B 916 " pdb=" CD1 LEU B 916 " pdb=" CD2 LEU B 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 4428 not shown) Planarity restraints: 4765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C ALA C 958 " 0.070 2.00e-02 2.50e+03 pdb=" O ALA C 958 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU C 959 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C ALA A 958 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 958 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 959 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 958 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ALA B 958 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA B 958 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 959 " 0.020 2.00e-02 2.50e+03 ... (remaining 4762 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1047 2.70 - 3.25: 25917 3.25 - 3.80: 43069 3.80 - 4.35: 55729 4.35 - 4.90: 94298 Nonbonded interactions: 220060 Sorted by model distance: nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLU C 516 " model vdw 2.156 2.440 nonbonded pdb=" NH2 ARG B 328 " pdb=" OE1 GLN B 580 " model vdw 2.183 2.520 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.206 2.440 nonbonded pdb=" ND2 ASN C 437 " pdb=" OE1 GLN C 506 " model vdw 2.209 2.520 nonbonded pdb=" NE2 GLN A 804 " pdb=" OE1 GLN A 935 " model vdw 2.213 2.520 ... (remaining 220055 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' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 or resid 1301 through 1308)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 throug \ h 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 or resid 140 \ 1 through 1408)) } ncs_group { reference = (chain 'D' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) selection = (chain 'E' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) selection = (chain 'F' and (resid 2 through 21 or resid 23 through 95 or resid 97 through 12 \ 6)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 5.270 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 72.490 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.340 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 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 : 0.007 0.079 27425 Z= 0.446 Angle : 0.883 12.451 37319 Z= 0.490 Chirality : 0.054 0.336 4431 Planarity : 0.004 0.056 4719 Dihedral : 13.005 86.194 10759 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 0.99 % Allowed : 4.66 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.88 (0.13), residues: 3290 helix: -0.39 (0.19), residues: 661 sheet: 0.05 (0.17), residues: 801 loop : -0.92 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 36 HIS 0.013 0.002 HIS C 519 PHE 0.033 0.003 PHE E 37 TYR 0.023 0.003 TYR B 495 ARG 0.021 0.002 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 451 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.6959 (m-80) cc_final: 0.6594 (m-80) REVERT: A 45 SER cc_start: 0.7951 (p) cc_final: 0.7747 (t) REVERT: A 120 VAL cc_start: 0.6438 (t) cc_final: 0.5971 (p) REVERT: A 129 LYS cc_start: 0.6586 (pttt) cc_final: 0.6373 (ptpt) REVERT: A 165 ASN cc_start: 0.5758 (m-40) cc_final: 0.4127 (t0) REVERT: A 230 PRO cc_start: 0.6957 (Cg_endo) cc_final: 0.6399 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6665 (ttm170) REVERT: A 309 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6978 (mm-30) REVERT: A 319 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7146 (ttm-80) REVERT: A 519 HIS cc_start: 0.4690 (OUTLIER) cc_final: 0.4366 (t70) REVERT: A 702 GLU cc_start: 0.7865 (pt0) cc_final: 0.7609 (tt0) REVERT: A 762 GLN cc_start: 0.7722 (tt0) cc_final: 0.7504 (mt0) REVERT: A 773 GLU cc_start: 0.6793 (tt0) cc_final: 0.6561 (tt0) REVERT: A 796 ASP cc_start: 0.6864 (t0) cc_final: 0.5814 (p0) REVERT: A 817 PHE cc_start: 0.7334 (t80) cc_final: 0.7022 (t80) REVERT: A 855 PHE cc_start: 0.7182 (m-80) cc_final: 0.6945 (m-80) REVERT: A 868 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7048 (mp0) REVERT: A 950 ASP cc_start: 0.7648 (t70) cc_final: 0.7185 (m-30) REVERT: A 1045 LYS cc_start: 0.7560 (mtpp) cc_final: 0.7346 (tttm) REVERT: A 1135 ASN cc_start: 0.8532 (t0) cc_final: 0.8318 (t0) REVERT: B 102 ARG cc_start: 0.6123 (mtt180) cc_final: 0.5809 (mmm160) REVERT: B 205 SER cc_start: 0.8441 (p) cc_final: 0.8149 (p) REVERT: B 269 TYR cc_start: 0.7343 (m-80) cc_final: 0.6998 (m-10) REVERT: B 271 GLN cc_start: 0.6757 (mt0) cc_final: 0.6292 (mm-40) REVERT: B 303 LEU cc_start: 0.6587 (mt) cc_final: 0.6235 (mp) REVERT: B 305 SER cc_start: 0.8584 (t) cc_final: 0.8361 (p) REVERT: B 316 SER cc_start: 0.7778 (t) cc_final: 0.7528 (p) REVERT: B 342 PHE cc_start: 0.7569 (m-80) cc_final: 0.7298 (m-80) REVERT: B 353 TRP cc_start: 0.7363 (p-90) cc_final: 0.6876 (p-90) REVERT: B 365 TYR cc_start: 0.6204 (m-80) cc_final: 0.5963 (m-80) REVERT: B 389 ASP cc_start: 0.7416 (m-30) cc_final: 0.6871 (t70) REVERT: B 453 TYR cc_start: 0.6791 (p90) cc_final: 0.6486 (p90) REVERT: B 508 TYR cc_start: 0.6223 (m-80) cc_final: 0.5678 (m-80) REVERT: B 592 PHE cc_start: 0.6697 (p90) cc_final: 0.6406 (p90) REVERT: B 646 ARG cc_start: 0.7509 (tpp80) cc_final: 0.6949 (mtp180) REVERT: B 658 ASN cc_start: 0.6819 (m-40) cc_final: 0.6453 (t0) REVERT: B 702 GLU cc_start: 0.8192 (tt0) cc_final: 0.7512 (mm-30) REVERT: B 773 GLU cc_start: 0.7030 (tt0) cc_final: 0.6725 (tt0) REVERT: B 790 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7405 (mmmt) REVERT: B 804 GLN cc_start: 0.8741 (mt0) cc_final: 0.8281 (mm110) REVERT: B 868 GLU cc_start: 0.7113 (pt0) cc_final: 0.6630 (mp0) REVERT: B 935 GLN cc_start: 0.6806 (mt0) cc_final: 0.6468 (mt0) REVERT: B 1010 GLN cc_start: 0.8127 (mm110) cc_final: 0.7907 (mm-40) REVERT: B 1038 LYS cc_start: 0.8291 (mttm) cc_final: 0.7940 (mmmt) REVERT: B 1045 LYS cc_start: 0.8358 (tttp) cc_final: 0.7765 (mptt) REVERT: B 1142 GLN cc_start: 0.6515 (mm-40) cc_final: 0.6295 (tt0) REVERT: C 45 SER cc_start: 0.7994 (p) cc_final: 0.7371 (t) REVERT: C 52 GLN cc_start: 0.7721 (tt0) cc_final: 0.7095 (tt0) REVERT: C 140 PHE cc_start: 0.5376 (p90) cc_final: 0.5131 (p90) REVERT: C 237 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7128 (mtm110) REVERT: C 307 THR cc_start: 0.7443 (p) cc_final: 0.7215 (p) REVERT: C 365 TYR cc_start: 0.6621 (m-80) cc_final: 0.6371 (m-80) REVERT: C 396 TYR cc_start: 0.6644 (m-80) cc_final: 0.6389 (m-80) REVERT: C 427 ASP cc_start: 0.7023 (m-30) cc_final: 0.6035 (t70) REVERT: C 512 VAL cc_start: 0.8162 (t) cc_final: 0.7762 (p) REVERT: C 558 LYS cc_start: 0.7337 (mmtt) cc_final: 0.7121 (mttm) REVERT: C 577 ARG cc_start: 0.6886 (ttm-80) cc_final: 0.6672 (ttm-80) REVERT: C 606 ASN cc_start: 0.8424 (m-40) cc_final: 0.8147 (m-40) REVERT: C 646 ARG cc_start: 0.8022 (mtt180) cc_final: 0.7397 (tpt90) REVERT: C 674 TYR cc_start: 0.8289 (t80) cc_final: 0.8040 (t80) REVERT: C 675 GLN cc_start: 0.7246 (mt0) cc_final: 0.6998 (mm-40) REVERT: C 755 GLN cc_start: 0.7642 (mt0) cc_final: 0.7141 (mm110) REVERT: C 758 SER cc_start: 0.6612 (m) cc_final: 0.6103 (p) REVERT: C 912 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 1005 GLN cc_start: 0.8072 (mt0) cc_final: 0.7767 (tp40) REVERT: C 1012 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8181 (mp) REVERT: C 1038 LYS cc_start: 0.8010 (mttm) cc_final: 0.7541 (mmtp) REVERT: C 1050 MET cc_start: 0.8853 (ptt) cc_final: 0.8641 (ptm) REVERT: C 1144 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6680 (mm-30) REVERT: F 29 PHE cc_start: 0.1969 (OUTLIER) cc_final: 0.1537 (t80) REVERT: F 83 MET cc_start: 0.2958 (mtp) cc_final: 0.1513 (tmm) outliers start: 27 outliers final: 10 residues processed: 473 average time/residue: 0.3943 time to fit residues: 287.9806 Evaluate side-chains 291 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 72 ARG Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain E residue 29 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 280 optimal weight: 0.8980 chunk 251 optimal weight: 0.0970 chunk 139 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 134 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 913 GLN B1002 GLN B1005 GLN B1101 HIS C 30 ASN C 125 ASN C 762 GLN C 804 GLN C 949 GLN C1002 GLN C1010 GLN C1048 HIS D 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 27425 Z= 0.172 Angle : 0.566 10.673 37319 Z= 0.294 Chirality : 0.045 0.285 4431 Planarity : 0.004 0.146 4719 Dihedral : 7.267 56.436 5017 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.52 % Allowed : 7.48 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3290 helix: 1.27 (0.21), residues: 655 sheet: 0.31 (0.16), residues: 830 loop : -0.39 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 117 HIS 0.009 0.001 HIS C 519 PHE 0.019 0.001 PHE C 592 TYR 0.031 0.001 TYR C 508 ARG 0.023 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7037 (t) cc_final: 0.6595 (p) REVERT: A 129 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6430 (ptpp) REVERT: A 165 ASN cc_start: 0.5653 (m-40) cc_final: 0.4018 (t0) REVERT: A 205 SER cc_start: 0.8046 (p) cc_final: 0.7781 (p) REVERT: A 237 ARG cc_start: 0.7030 (ttm-80) cc_final: 0.6736 (ttm170) REVERT: A 309 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6781 (mm-30) REVERT: A 314 GLN cc_start: 0.8461 (tt0) cc_final: 0.8176 (tm-30) REVERT: A 554 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7066 (mm-30) REVERT: A 586 ASP cc_start: 0.8115 (m-30) cc_final: 0.7905 (m-30) REVERT: A 646 ARG cc_start: 0.7651 (tpp80) cc_final: 0.7216 (mtm180) REVERT: A 654 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6930 (tp30) REVERT: A 702 GLU cc_start: 0.7780 (pt0) cc_final: 0.7512 (tt0) REVERT: A 704 SER cc_start: 0.8436 (p) cc_final: 0.8151 (m) REVERT: A 762 GLN cc_start: 0.7816 (tt0) cc_final: 0.7535 (mt0) REVERT: A 796 ASP cc_start: 0.6600 (t0) cc_final: 0.5528 (p0) REVERT: A 817 PHE cc_start: 0.7212 (t80) cc_final: 0.6848 (t80) REVERT: A 868 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7134 (mp0) REVERT: A 912 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 950 ASP cc_start: 0.7617 (t70) cc_final: 0.7260 (m-30) REVERT: A 1019 ARG cc_start: 0.7460 (ttp80) cc_final: 0.7053 (ttm110) REVERT: A 1045 LYS cc_start: 0.7603 (mtpp) cc_final: 0.7214 (mmtt) REVERT: B 102 ARG cc_start: 0.5916 (mtt180) cc_final: 0.5709 (mtp180) REVERT: B 205 SER cc_start: 0.8496 (p) cc_final: 0.8227 (t) REVERT: B 271 GLN cc_start: 0.6431 (mt0) cc_final: 0.6028 (mm110) REVERT: B 316 SER cc_start: 0.7904 (t) cc_final: 0.7387 (p) REVERT: B 317 ASN cc_start: 0.8264 (m-40) cc_final: 0.8044 (m110) REVERT: B 342 PHE cc_start: 0.7570 (m-80) cc_final: 0.7102 (m-80) REVERT: B 389 ASP cc_start: 0.7371 (m-30) cc_final: 0.6919 (t70) REVERT: B 465 GLU cc_start: 0.7262 (tp30) cc_final: 0.7023 (tp30) REVERT: B 507 PRO cc_start: 0.5932 (Cg_exo) cc_final: 0.5353 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6106 (m-80) cc_final: 0.5182 (m-80) REVERT: B 646 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7128 (mtp180) REVERT: B 658 ASN cc_start: 0.6714 (m-40) cc_final: 0.6297 (t0) REVERT: B 702 GLU cc_start: 0.8242 (tt0) cc_final: 0.7625 (mm-30) REVERT: B 750 SER cc_start: 0.6965 (t) cc_final: 0.6735 (m) REVERT: B 773 GLU cc_start: 0.6955 (tt0) cc_final: 0.6609 (tt0) REVERT: B 776 LYS cc_start: 0.7181 (tttt) cc_final: 0.6952 (tttm) REVERT: B 790 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7339 (mmmt) REVERT: B 804 GLN cc_start: 0.8792 (mt0) cc_final: 0.8316 (mm110) REVERT: B 825 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6384 (mtpt) REVERT: B 868 GLU cc_start: 0.7343 (pt0) cc_final: 0.6730 (mp0) REVERT: B 950 ASP cc_start: 0.7246 (t70) cc_final: 0.6775 (m-30) REVERT: B 960 ASN cc_start: 0.6973 (m-40) cc_final: 0.6498 (t0) REVERT: B 1038 LYS cc_start: 0.8325 (mttm) cc_final: 0.7950 (mmmt) REVERT: B 1045 LYS cc_start: 0.8626 (tttp) cc_final: 0.7957 (mptt) REVERT: B 1142 GLN cc_start: 0.6574 (mm-40) cc_final: 0.6369 (tt0) REVERT: C 45 SER cc_start: 0.7985 (p) cc_final: 0.7444 (t) REVERT: C 65 PHE cc_start: 0.7074 (m-80) cc_final: 0.6633 (m-80) REVERT: C 140 PHE cc_start: 0.5647 (p90) cc_final: 0.5356 (p90) REVERT: C 237 ARG cc_start: 0.7523 (mtt180) cc_final: 0.6965 (mtm110) REVERT: C 304 LYS cc_start: 0.7200 (mptt) cc_final: 0.6830 (mtpt) REVERT: C 427 ASP cc_start: 0.6923 (m-30) cc_final: 0.6003 (t70) REVERT: C 433 VAL cc_start: 0.7120 (t) cc_final: 0.6794 (p) REVERT: C 434 ILE cc_start: 0.6115 (mp) cc_final: 0.5685 (mm) REVERT: C 532 ASN cc_start: 0.6204 (t0) cc_final: 0.5812 (p0) REVERT: C 577 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: C 606 ASN cc_start: 0.8413 (m-40) cc_final: 0.8194 (m-40) REVERT: C 646 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7487 (tpt90) REVERT: C 740 MET cc_start: 0.8137 (ttt) cc_final: 0.7925 (ttm) REVERT: C 755 GLN cc_start: 0.7725 (mt0) cc_final: 0.7224 (mm110) REVERT: C 912 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7981 (p) REVERT: C 1005 GLN cc_start: 0.8005 (mt0) cc_final: 0.7799 (tp40) REVERT: C 1038 LYS cc_start: 0.7968 (mttm) cc_final: 0.7490 (mmtp) REVERT: C 1045 LYS cc_start: 0.8478 (tttt) cc_final: 0.8236 (ttmt) REVERT: C 1081 ILE cc_start: 0.7452 (pt) cc_final: 0.7182 (pt) REVERT: C 1144 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6775 (mm-30) REVERT: F 29 PHE cc_start: 0.2355 (OUTLIER) cc_final: 0.1999 (t80) REVERT: F 83 MET cc_start: 0.2569 (mtp) cc_final: 0.1402 (tmm) REVERT: E 34 MET cc_start: 0.4390 (mtm) cc_final: 0.3976 (mtm) outliers start: 42 outliers final: 20 residues processed: 359 average time/residue: 0.4073 time to fit residues: 231.4157 Evaluate side-chains 301 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 277 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain D residue 27 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 167 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 250 optimal weight: 0.0980 chunk 205 optimal weight: 0.0010 chunk 83 optimal weight: 0.5980 chunk 302 optimal weight: 6.9990 chunk 326 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 935 GLN A1005 GLN A1048 HIS B 314 GLN B 613 GLN B 762 GLN B 954 GLN B1002 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 901 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 27425 Z= 0.150 Angle : 0.517 13.210 37319 Z= 0.267 Chirality : 0.043 0.429 4431 Planarity : 0.003 0.084 4719 Dihedral : 6.188 55.891 4998 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.91 % Allowed : 8.68 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.52 (0.14), residues: 3290 helix: 2.01 (0.21), residues: 639 sheet: 0.39 (0.17), residues: 855 loop : -0.24 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 53 HIS 0.008 0.001 HIS C 519 PHE 0.020 0.001 PHE B 329 TYR 0.021 0.001 TYR E 95 ARG 0.007 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7641 (m-40) cc_final: 0.7089 (p0) REVERT: A 120 VAL cc_start: 0.6967 (t) cc_final: 0.6450 (p) REVERT: A 129 LYS cc_start: 0.6673 (pttt) cc_final: 0.6394 (ptpt) REVERT: A 165 ASN cc_start: 0.5558 (m-40) cc_final: 0.4040 (t0) REVERT: A 205 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 237 ARG cc_start: 0.7006 (ttm-80) cc_final: 0.6680 (ttm170) REVERT: A 309 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6838 (mm-30) REVERT: A 314 GLN cc_start: 0.8420 (tt0) cc_final: 0.8144 (tm-30) REVERT: A 554 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7073 (mm-30) REVERT: A 646 ARG cc_start: 0.7664 (tpp80) cc_final: 0.7194 (mtm180) REVERT: A 702 GLU cc_start: 0.7776 (pt0) cc_final: 0.7493 (tt0) REVERT: A 704 SER cc_start: 0.8483 (p) cc_final: 0.8216 (m) REVERT: A 758 SER cc_start: 0.7014 (m) cc_final: 0.6616 (p) REVERT: A 762 GLN cc_start: 0.7823 (tt0) cc_final: 0.7555 (mt0) REVERT: A 796 ASP cc_start: 0.6541 (t0) cc_final: 0.5417 (p0) REVERT: A 817 PHE cc_start: 0.7263 (t80) cc_final: 0.6865 (t80) REVERT: A 868 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7183 (mp0) REVERT: A 950 ASP cc_start: 0.7568 (t70) cc_final: 0.7262 (m-30) REVERT: A 1019 ARG cc_start: 0.7395 (ttp80) cc_final: 0.6893 (ttp-110) REVERT: A 1045 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7306 (mmtt) REVERT: B 207 HIS cc_start: 0.6272 (t-90) cc_final: 0.6057 (t-90) REVERT: B 269 TYR cc_start: 0.7546 (m-10) cc_final: 0.7260 (m-80) REVERT: B 271 GLN cc_start: 0.6329 (mt0) cc_final: 0.5955 (mm110) REVERT: B 316 SER cc_start: 0.7838 (t) cc_final: 0.7275 (p) REVERT: B 317 ASN cc_start: 0.8252 (m-40) cc_final: 0.8028 (m110) REVERT: B 342 PHE cc_start: 0.7588 (m-80) cc_final: 0.7065 (m-80) REVERT: B 351 TYR cc_start: 0.7504 (p90) cc_final: 0.7273 (p90) REVERT: B 389 ASP cc_start: 0.7364 (m-30) cc_final: 0.6847 (t0) REVERT: B 434 ILE cc_start: 0.7039 (mt) cc_final: 0.6749 (mt) REVERT: B 465 GLU cc_start: 0.7188 (tp30) cc_final: 0.6986 (tp30) REVERT: B 507 PRO cc_start: 0.5962 (Cg_exo) cc_final: 0.5415 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6044 (m-80) cc_final: 0.5163 (m-80) REVERT: B 646 ARG cc_start: 0.7502 (tpp80) cc_final: 0.7129 (mtp180) REVERT: B 658 ASN cc_start: 0.7005 (m-40) cc_final: 0.6572 (t0) REVERT: B 702 GLU cc_start: 0.8245 (tt0) cc_final: 0.7658 (mm-30) REVERT: B 750 SER cc_start: 0.7010 (t) cc_final: 0.6780 (m) REVERT: B 773 GLU cc_start: 0.7059 (tt0) cc_final: 0.6751 (tt0) REVERT: B 776 LYS cc_start: 0.7140 (tttt) cc_final: 0.6877 (ttpp) REVERT: B 790 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7368 (mmmt) REVERT: B 804 GLN cc_start: 0.8586 (mt0) cc_final: 0.8157 (mm110) REVERT: B 825 LYS cc_start: 0.6783 (mmtt) cc_final: 0.6412 (mtpt) REVERT: B 868 GLU cc_start: 0.7404 (pt0) cc_final: 0.6762 (mp0) REVERT: B 950 ASP cc_start: 0.7262 (t70) cc_final: 0.6733 (m-30) REVERT: B 954 GLN cc_start: 0.7685 (mt0) cc_final: 0.7463 (mt0) REVERT: B 960 ASN cc_start: 0.6915 (m-40) cc_final: 0.6478 (t0) REVERT: B 1038 LYS cc_start: 0.8242 (mttm) cc_final: 0.7840 (mmmt) REVERT: B 1142 GLN cc_start: 0.6321 (mm-40) cc_final: 0.6087 (tt0) REVERT: C 45 SER cc_start: 0.8069 (p) cc_final: 0.7500 (t) REVERT: C 65 PHE cc_start: 0.7151 (m-80) cc_final: 0.6698 (m-80) REVERT: C 140 PHE cc_start: 0.5815 (p90) cc_final: 0.5502 (p90) REVERT: C 237 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6787 (ttp-170) REVERT: C 304 LYS cc_start: 0.7220 (mptt) cc_final: 0.6950 (mtpt) REVERT: C 427 ASP cc_start: 0.6945 (m-30) cc_final: 0.5998 (t70) REVERT: C 433 VAL cc_start: 0.7049 (t) cc_final: 0.6726 (p) REVERT: C 434 ILE cc_start: 0.6094 (mp) cc_final: 0.5742 (mm) REVERT: C 508 TYR cc_start: 0.6194 (m-80) cc_final: 0.5510 (m-80) REVERT: C 532 ASN cc_start: 0.6277 (t0) cc_final: 0.5859 (p0) REVERT: C 577 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6805 (ttm-80) REVERT: C 606 ASN cc_start: 0.8408 (m-40) cc_final: 0.8182 (m-40) REVERT: C 646 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7432 (tpt90) REVERT: C 755 GLN cc_start: 0.7752 (mt0) cc_final: 0.7221 (mm110) REVERT: C 912 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8028 (p) REVERT: C 1005 GLN cc_start: 0.7980 (mt0) cc_final: 0.7730 (tp-100) REVERT: C 1038 LYS cc_start: 0.8010 (mttm) cc_final: 0.7519 (mmtp) REVERT: C 1045 LYS cc_start: 0.8537 (tttt) cc_final: 0.8293 (ttmt) REVERT: C 1081 ILE cc_start: 0.7348 (pt) cc_final: 0.7092 (pt) REVERT: C 1144 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6799 (mm-30) REVERT: F 34 MET cc_start: 0.3348 (mpp) cc_final: 0.2548 (mpp) REVERT: F 83 MET cc_start: 0.2771 (mtp) cc_final: 0.1476 (tmm) REVERT: E 34 MET cc_start: 0.4412 (mtm) cc_final: 0.3945 (mtm) outliers start: 52 outliers final: 28 residues processed: 341 average time/residue: 0.3785 time to fit residues: 207.0387 Evaluate side-chains 303 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 273 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain F residue 29 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 298 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 239 GLN B 314 GLN B 317 ASN B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN B 762 GLN B1106 GLN B1119 ASN C 125 ASN C 239 GLN C 450 ASN C 935 GLN C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 27425 Z= 0.494 Angle : 0.712 13.751 37319 Z= 0.363 Chirality : 0.051 0.661 4431 Planarity : 0.005 0.068 4719 Dihedral : 6.928 59.438 4994 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.14 % Allowed : 8.65 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.07 (0.14), residues: 3290 helix: 1.34 (0.20), residues: 640 sheet: 0.23 (0.16), residues: 865 loop : -0.48 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.008 0.002 HIS C 519 PHE 0.023 0.003 PHE A 32 TYR 0.025 0.002 TYR E 95 ARG 0.009 0.001 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 277 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7620 (m-40) cc_final: 0.7196 (p0) REVERT: A 106 PHE cc_start: 0.7494 (m-80) cc_final: 0.7170 (m-80) REVERT: A 120 VAL cc_start: 0.6996 (t) cc_final: 0.6533 (p) REVERT: A 129 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6443 (ptpt) REVERT: A 205 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 237 ARG cc_start: 0.7062 (ttm-80) cc_final: 0.6827 (ttp80) REVERT: A 309 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6845 (mm-30) REVERT: A 646 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7263 (mtm180) REVERT: A 702 GLU cc_start: 0.7772 (pt0) cc_final: 0.7471 (tt0) REVERT: A 704 SER cc_start: 0.8569 (p) cc_final: 0.8293 (m) REVERT: A 762 GLN cc_start: 0.7927 (tt0) cc_final: 0.7638 (mt0) REVERT: A 776 LYS cc_start: 0.6996 (tttt) cc_final: 0.6699 (ttpp) REVERT: A 817 PHE cc_start: 0.7432 (t80) cc_final: 0.7040 (t80) REVERT: A 868 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7208 (mp0) REVERT: A 950 ASP cc_start: 0.7829 (t70) cc_final: 0.7428 (m-30) REVERT: A 1045 LYS cc_start: 0.7677 (mtpp) cc_final: 0.7273 (mmtt) REVERT: B 102 ARG cc_start: 0.6287 (mtp180) cc_final: 0.6070 (mmm-85) REVERT: B 271 GLN cc_start: 0.6244 (mt0) cc_final: 0.5918 (mm110) REVERT: B 324 GLU cc_start: 0.5839 (mm-30) cc_final: 0.5631 (tt0) REVERT: B 389 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7159 (t70) REVERT: B 465 GLU cc_start: 0.7072 (tp30) cc_final: 0.6870 (tp30) REVERT: B 507 PRO cc_start: 0.5858 (Cg_exo) cc_final: 0.5334 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6404 (m-80) cc_final: 0.5648 (m-80) REVERT: B 529 LYS cc_start: 0.6802 (mttm) cc_final: 0.6494 (mtmm) REVERT: B 574 ASP cc_start: 0.7235 (t0) cc_final: 0.6941 (t0) REVERT: B 591 SER cc_start: 0.7685 (t) cc_final: 0.7466 (m) REVERT: B 646 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7129 (ttm170) REVERT: B 658 ASN cc_start: 0.6996 (m-40) cc_final: 0.6510 (t0) REVERT: B 702 GLU cc_start: 0.8420 (tt0) cc_final: 0.7759 (mm-30) REVERT: B 776 LYS cc_start: 0.7445 (tttt) cc_final: 0.7224 (tttm) REVERT: B 790 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7459 (mmmt) REVERT: B 804 GLN cc_start: 0.8524 (mt0) cc_final: 0.7931 (mm110) REVERT: B 825 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6454 (mtpt) REVERT: B 868 GLU cc_start: 0.7034 (pt0) cc_final: 0.6579 (mp0) REVERT: B 950 ASP cc_start: 0.7070 (t70) cc_final: 0.6824 (m-30) REVERT: B 960 ASN cc_start: 0.7232 (m-40) cc_final: 0.6601 (t0) REVERT: B 1038 LYS cc_start: 0.8276 (mttm) cc_final: 0.7905 (mmmt) REVERT: B 1142 GLN cc_start: 0.6484 (mm-40) cc_final: 0.6220 (tt0) REVERT: C 33 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7641 (p) REVERT: C 45 SER cc_start: 0.8218 (p) cc_final: 0.7685 (t) REVERT: C 65 PHE cc_start: 0.6972 (m-80) cc_final: 0.6461 (m-80) REVERT: C 140 PHE cc_start: 0.5777 (p90) cc_final: 0.5447 (p90) REVERT: C 196 ASN cc_start: 0.7731 (t0) cc_final: 0.7451 (m-40) REVERT: C 237 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6919 (mtm110) REVERT: C 433 VAL cc_start: 0.7170 (t) cc_final: 0.6885 (p) REVERT: C 508 TYR cc_start: 0.6384 (m-80) cc_final: 0.5615 (m-80) REVERT: C 577 ARG cc_start: 0.7026 (ttm-80) cc_final: 0.6565 (ttm-80) REVERT: C 606 ASN cc_start: 0.8483 (m-40) cc_final: 0.8225 (m-40) REVERT: C 646 ARG cc_start: 0.7952 (mtt180) cc_final: 0.7336 (tpt90) REVERT: C 755 GLN cc_start: 0.7614 (mt0) cc_final: 0.7194 (mm-40) REVERT: C 758 SER cc_start: 0.6676 (m) cc_final: 0.6269 (p) REVERT: C 804 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7734 (mt0) REVERT: C 912 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8018 (p) REVERT: C 1012 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8275 (mp) REVERT: C 1038 LYS cc_start: 0.8045 (mttm) cc_final: 0.7478 (mmtp) REVERT: C 1045 LYS cc_start: 0.8380 (tttt) cc_final: 0.8119 (ttmt) REVERT: E 34 MET cc_start: 0.4441 (mtm) cc_final: 0.3886 (mtm) outliers start: 87 outliers final: 58 residues processed: 347 average time/residue: 0.3732 time to fit residues: 207.6264 Evaluate side-chains 313 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 267 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 238 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 273 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 955 ASN A1005 GLN B 314 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B1002 GLN C 125 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27425 Z= 0.173 Angle : 0.530 12.319 37319 Z= 0.274 Chirality : 0.044 0.468 4431 Planarity : 0.003 0.056 4719 Dihedral : 6.059 58.902 4992 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.80 % Allowed : 10.73 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.14), residues: 3290 helix: 1.79 (0.21), residues: 639 sheet: 0.22 (0.16), residues: 858 loop : -0.37 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.006 0.001 HIS C 519 PHE 0.021 0.001 PHE C 400 TYR 0.022 0.001 TYR E 95 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 268 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.6964 (t) cc_final: 0.6506 (p) REVERT: A 129 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6275 (ptpp) REVERT: A 188 ASN cc_start: 0.6215 (m-40) cc_final: 0.5401 (p0) REVERT: A 237 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6752 (ttm170) REVERT: A 269 TYR cc_start: 0.8122 (m-80) cc_final: 0.7794 (m-80) REVERT: A 309 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6920 (mm-30) REVERT: A 319 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7385 (ttm-80) REVERT: A 646 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7270 (mtm180) REVERT: A 654 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7083 (tp30) REVERT: A 702 GLU cc_start: 0.7815 (pt0) cc_final: 0.7564 (tt0) REVERT: A 704 SER cc_start: 0.8622 (p) cc_final: 0.8325 (m) REVERT: A 762 GLN cc_start: 0.7852 (tt0) cc_final: 0.7649 (mt0) REVERT: A 817 PHE cc_start: 0.7336 (t80) cc_final: 0.6933 (t80) REVERT: A 868 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7155 (mp0) REVERT: A 950 ASP cc_start: 0.7742 (t70) cc_final: 0.7438 (m-30) REVERT: A 1045 LYS cc_start: 0.7640 (mtpp) cc_final: 0.7241 (mmtt) REVERT: B 271 GLN cc_start: 0.6049 (mt0) cc_final: 0.5751 (mm110) REVERT: B 316 SER cc_start: 0.8206 (t) cc_final: 0.7700 (p) REVERT: B 389 ASP cc_start: 0.7616 (m-30) cc_final: 0.7143 (t0) REVERT: B 390 LEU cc_start: 0.8108 (mt) cc_final: 0.7873 (mt) REVERT: B 465 GLU cc_start: 0.7147 (tp30) cc_final: 0.6894 (tp30) REVERT: B 507 PRO cc_start: 0.5971 (Cg_exo) cc_final: 0.5490 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6288 (m-80) cc_final: 0.5513 (m-80) REVERT: B 529 LYS cc_start: 0.6829 (mttm) cc_final: 0.6497 (mtmm) REVERT: B 574 ASP cc_start: 0.7250 (t0) cc_final: 0.6927 (t0) REVERT: B 646 ARG cc_start: 0.7468 (tpp80) cc_final: 0.7158 (ttm170) REVERT: B 658 ASN cc_start: 0.6886 (m-40) cc_final: 0.6431 (t0) REVERT: B 702 GLU cc_start: 0.8283 (tt0) cc_final: 0.7699 (mm-30) REVERT: B 776 LYS cc_start: 0.7191 (tttt) cc_final: 0.6971 (tttm) REVERT: B 790 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7471 (mmmt) REVERT: B 804 GLN cc_start: 0.8571 (mt0) cc_final: 0.8103 (mm110) REVERT: B 825 LYS cc_start: 0.6806 (mmtt) cc_final: 0.6357 (mtpt) REVERT: B 868 GLU cc_start: 0.7230 (pt0) cc_final: 0.6730 (mp0) REVERT: B 935 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6268 (mt0) REVERT: B 950 ASP cc_start: 0.6976 (t70) cc_final: 0.6621 (m-30) REVERT: B 954 GLN cc_start: 0.7707 (mt0) cc_final: 0.7482 (mt0) REVERT: B 960 ASN cc_start: 0.7256 (m-40) cc_final: 0.6739 (t0) REVERT: B 1038 LYS cc_start: 0.8332 (mttm) cc_final: 0.7966 (mmmt) REVERT: C 45 SER cc_start: 0.8147 (p) cc_final: 0.7616 (t) REVERT: C 65 PHE cc_start: 0.7028 (m-80) cc_final: 0.6420 (m-80) REVERT: C 140 PHE cc_start: 0.5797 (p90) cc_final: 0.5460 (p90) REVERT: C 224 GLU cc_start: 0.7493 (pm20) cc_final: 0.7193 (mt-10) REVERT: C 237 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7134 (mtm110) REVERT: C 433 VAL cc_start: 0.7101 (t) cc_final: 0.6643 (p) REVERT: C 508 TYR cc_start: 0.6362 (m-80) cc_final: 0.6124 (m-80) REVERT: C 577 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6742 (ttm-80) REVERT: C 606 ASN cc_start: 0.8452 (m-40) cc_final: 0.8200 (m-40) REVERT: C 646 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7246 (tpt90) REVERT: C 755 GLN cc_start: 0.7749 (mt0) cc_final: 0.7225 (mm110) REVERT: C 817 PHE cc_start: 0.7176 (t80) cc_final: 0.6878 (t80) REVERT: C 912 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7940 (p) REVERT: C 1038 LYS cc_start: 0.8037 (mttm) cc_final: 0.7470 (mmtp) REVERT: C 1045 LYS cc_start: 0.8458 (tttt) cc_final: 0.8212 (ttmt) REVERT: C 1081 ILE cc_start: 0.7422 (pt) cc_final: 0.7145 (pt) REVERT: F 29 PHE cc_start: 0.1951 (OUTLIER) cc_final: 0.1544 (t80) REVERT: E 12 MET cc_start: 0.3213 (ppp) cc_final: 0.2955 (ppp) REVERT: E 34 MET cc_start: 0.4564 (mtm) cc_final: 0.3969 (mtm) outliers start: 49 outliers final: 28 residues processed: 306 average time/residue: 0.3859 time to fit residues: 188.0512 Evaluate side-chains 284 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain F residue 29 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 107 optimal weight: 10.0000 chunk 288 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 321 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 901 GLN A1005 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1002 GLN C 774 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 27425 Z= 0.334 Angle : 0.597 12.610 37319 Z= 0.304 Chirality : 0.046 0.596 4431 Planarity : 0.004 0.051 4719 Dihedral : 6.051 59.860 4992 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.65 % Allowed : 10.23 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.16 (0.14), residues: 3290 helix: 1.64 (0.21), residues: 639 sheet: 0.19 (0.16), residues: 865 loop : -0.46 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.007 0.001 HIS C 519 PHE 0.016 0.002 PHE C1121 TYR 0.023 0.002 TYR E 95 ARG 0.006 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 256 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7700 (m-40) cc_final: 0.7166 (p0) REVERT: A 120 VAL cc_start: 0.7005 (t) cc_final: 0.6564 (p) REVERT: A 129 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6375 (ptpp) REVERT: A 205 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 237 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6729 (ttm170) REVERT: A 269 TYR cc_start: 0.7967 (m-80) cc_final: 0.7676 (m-80) REVERT: A 309 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6900 (mm-30) REVERT: A 646 ARG cc_start: 0.7779 (tpp80) cc_final: 0.7268 (mtm180) REVERT: A 702 GLU cc_start: 0.7775 (pt0) cc_final: 0.7506 (tt0) REVERT: A 704 SER cc_start: 0.8518 (p) cc_final: 0.8251 (m) REVERT: A 762 GLN cc_start: 0.7933 (tt0) cc_final: 0.7676 (mt0) REVERT: A 776 LYS cc_start: 0.6938 (tttt) cc_final: 0.6712 (ttpp) REVERT: A 817 PHE cc_start: 0.7406 (t80) cc_final: 0.6995 (t80) REVERT: A 868 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7148 (mp0) REVERT: A 950 ASP cc_start: 0.7817 (t70) cc_final: 0.7529 (m-30) REVERT: A 1045 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7231 (mmtt) REVERT: B 271 GLN cc_start: 0.6109 (mt0) cc_final: 0.5864 (mm110) REVERT: B 507 PRO cc_start: 0.5926 (Cg_exo) cc_final: 0.5463 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6348 (m-80) cc_final: 0.5553 (m-80) REVERT: B 529 LYS cc_start: 0.7263 (mttm) cc_final: 0.6958 (mtmm) REVERT: B 574 ASP cc_start: 0.7275 (t0) cc_final: 0.6936 (t0) REVERT: B 646 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7103 (ttm170) REVERT: B 658 ASN cc_start: 0.6925 (m-40) cc_final: 0.6433 (t0) REVERT: B 702 GLU cc_start: 0.8389 (tt0) cc_final: 0.7760 (mm-30) REVERT: B 776 LYS cc_start: 0.7272 (tttt) cc_final: 0.7045 (tttm) REVERT: B 790 LYS cc_start: 0.7768 (ttpt) cc_final: 0.7452 (mmmt) REVERT: B 804 GLN cc_start: 0.8569 (mt0) cc_final: 0.8055 (mm110) REVERT: B 825 LYS cc_start: 0.6958 (mmtt) cc_final: 0.6529 (mtpt) REVERT: B 868 GLU cc_start: 0.7121 (pt0) cc_final: 0.6661 (mp0) REVERT: B 935 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6224 (mt0) REVERT: B 950 ASP cc_start: 0.6965 (t70) cc_final: 0.6687 (m-30) REVERT: B 960 ASN cc_start: 0.7300 (m-40) cc_final: 0.6726 (t0) REVERT: B 1038 LYS cc_start: 0.8250 (mttm) cc_final: 0.7885 (mmmt) REVERT: C 33 THR cc_start: 0.7935 (m) cc_final: 0.7653 (p) REVERT: C 45 SER cc_start: 0.8198 (p) cc_final: 0.7679 (t) REVERT: C 140 PHE cc_start: 0.5653 (p90) cc_final: 0.5333 (p90) REVERT: C 196 ASN cc_start: 0.7951 (t0) cc_final: 0.7390 (m-40) REVERT: C 224 GLU cc_start: 0.7441 (pm20) cc_final: 0.7175 (pm20) REVERT: C 237 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7101 (mtm110) REVERT: C 433 VAL cc_start: 0.7165 (t) cc_final: 0.6867 (p) REVERT: C 508 TYR cc_start: 0.6445 (m-80) cc_final: 0.5750 (m-80) REVERT: C 606 ASN cc_start: 0.8436 (m-40) cc_final: 0.8183 (m-40) REVERT: C 646 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7405 (tpt90) REVERT: C 755 GLN cc_start: 0.7638 (mt0) cc_final: 0.7119 (mm110) REVERT: C 804 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7753 (mt0) REVERT: C 912 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.7980 (p) REVERT: C 1038 LYS cc_start: 0.8044 (mttm) cc_final: 0.7482 (mmtp) REVERT: C 1045 LYS cc_start: 0.8419 (tttt) cc_final: 0.8172 (ttmt) REVERT: C 1081 ILE cc_start: 0.7448 (pt) cc_final: 0.7178 (pt) REVERT: D 34 MET cc_start: 0.2320 (ptt) cc_final: 0.1804 (ptm) REVERT: E 12 MET cc_start: 0.3264 (ppp) cc_final: 0.3027 (ppp) REVERT: E 34 MET cc_start: 0.4703 (mtm) cc_final: 0.4070 (mtm) outliers start: 72 outliers final: 52 residues processed: 311 average time/residue: 0.3791 time to fit residues: 190.4729 Evaluate side-chains 306 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 309 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 179 optimal weight: 0.1980 chunk 319 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 195 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 27425 Z= 0.225 Angle : 0.542 10.097 37319 Z= 0.278 Chirality : 0.045 0.612 4431 Planarity : 0.003 0.045 4719 Dihedral : 5.720 57.930 4992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.36 % Allowed : 10.44 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.14), residues: 3290 helix: 1.85 (0.21), residues: 632 sheet: 0.15 (0.17), residues: 847 loop : -0.43 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 353 HIS 0.006 0.001 HIS C 519 PHE 0.015 0.001 PHE B 565 TYR 0.021 0.001 TYR E 95 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 264 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.6973 (t) cc_final: 0.6522 (p) REVERT: A 129 LYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6326 (ptpp) REVERT: A 205 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 230 PRO cc_start: 0.7155 (Cg_endo) cc_final: 0.6781 (Cg_exo) REVERT: A 237 ARG cc_start: 0.7061 (ttm-80) cc_final: 0.6719 (ttm170) REVERT: A 269 TYR cc_start: 0.7940 (m-80) cc_final: 0.7628 (m-80) REVERT: A 309 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6926 (mm-30) REVERT: A 646 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7265 (mtm180) REVERT: A 702 GLU cc_start: 0.7757 (pt0) cc_final: 0.7551 (tt0) REVERT: A 704 SER cc_start: 0.8509 (p) cc_final: 0.8251 (m) REVERT: A 776 LYS cc_start: 0.6973 (tttt) cc_final: 0.6579 (ttpp) REVERT: A 817 PHE cc_start: 0.7379 (t80) cc_final: 0.6947 (t80) REVERT: A 868 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7165 (mp0) REVERT: A 950 ASP cc_start: 0.7753 (t70) cc_final: 0.7447 (m-30) REVERT: A 1045 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7239 (mmtt) REVERT: B 271 GLN cc_start: 0.6102 (mt0) cc_final: 0.5847 (mm110) REVERT: B 507 PRO cc_start: 0.5824 (Cg_exo) cc_final: 0.5388 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6329 (m-80) cc_final: 0.5535 (m-80) REVERT: B 529 LYS cc_start: 0.7278 (mttm) cc_final: 0.6977 (mtmm) REVERT: B 574 ASP cc_start: 0.7338 (t0) cc_final: 0.7028 (t0) REVERT: B 646 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7118 (ttm170) REVERT: B 657 ASN cc_start: 0.7383 (t0) cc_final: 0.7015 (t0) REVERT: B 658 ASN cc_start: 0.6824 (m-40) cc_final: 0.6315 (t0) REVERT: B 702 GLU cc_start: 0.8324 (tt0) cc_final: 0.7766 (mm-30) REVERT: B 776 LYS cc_start: 0.7212 (tttt) cc_final: 0.6987 (tttm) REVERT: B 790 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7444 (mmtt) REVERT: B 804 GLN cc_start: 0.8570 (mt0) cc_final: 0.8051 (mm110) REVERT: B 825 LYS cc_start: 0.6883 (mmtt) cc_final: 0.6434 (mtpt) REVERT: B 868 GLU cc_start: 0.7127 (pt0) cc_final: 0.6662 (mp0) REVERT: B 935 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.6273 (mt0) REVERT: B 950 ASP cc_start: 0.6896 (t70) cc_final: 0.6590 (m-30) REVERT: B 954 GLN cc_start: 0.7672 (mt0) cc_final: 0.7461 (mt0) REVERT: B 960 ASN cc_start: 0.7374 (m-40) cc_final: 0.6724 (t0) REVERT: B 1038 LYS cc_start: 0.8234 (mttm) cc_final: 0.7872 (mmmt) REVERT: C 45 SER cc_start: 0.8232 (p) cc_final: 0.7705 (t) REVERT: C 140 PHE cc_start: 0.5631 (p90) cc_final: 0.5331 (p90) REVERT: C 196 ASN cc_start: 0.7906 (t0) cc_final: 0.7378 (m-40) REVERT: C 224 GLU cc_start: 0.7504 (pm20) cc_final: 0.7228 (mt-10) REVERT: C 237 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7110 (mtm110) REVERT: C 433 VAL cc_start: 0.7116 (t) cc_final: 0.6826 (p) REVERT: C 508 TYR cc_start: 0.6295 (m-80) cc_final: 0.5639 (m-80) REVERT: C 606 ASN cc_start: 0.8423 (m-40) cc_final: 0.8184 (m-40) REVERT: C 646 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7224 (tpt90) REVERT: C 755 GLN cc_start: 0.7637 (mt0) cc_final: 0.7122 (mm110) REVERT: C 804 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7781 (mt0) REVERT: C 912 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7931 (p) REVERT: C 1038 LYS cc_start: 0.8043 (mttm) cc_final: 0.7481 (mmtp) REVERT: C 1045 LYS cc_start: 0.8444 (tttt) cc_final: 0.8191 (ttmt) REVERT: C 1081 ILE cc_start: 0.7425 (pt) cc_final: 0.7159 (pt) REVERT: E 34 MET cc_start: 0.4629 (mtm) cc_final: 0.4013 (mtm) outliers start: 63 outliers final: 50 residues processed: 308 average time/residue: 0.3728 time to fit residues: 184.2256 Evaluate side-chains 299 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 245 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 935 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 218 optimal weight: 0.0270 chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 251 optimal weight: 0.5980 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 935 GLN F 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27425 Z= 0.233 Angle : 0.539 9.530 37319 Z= 0.276 Chirality : 0.045 0.477 4431 Planarity : 0.003 0.042 4719 Dihedral : 5.560 56.187 4992 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 10.76 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.24 (0.14), residues: 3290 helix: 1.86 (0.21), residues: 633 sheet: 0.13 (0.17), residues: 858 loop : -0.41 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.006 0.001 HIS C 519 PHE 0.025 0.001 PHE A 592 TYR 0.021 0.001 TYR E 95 ARG 0.007 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 253 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7573 (m-40) cc_final: 0.6976 (p0) REVERT: A 129 LYS cc_start: 0.6761 (OUTLIER) cc_final: 0.6373 (ptpp) REVERT: A 230 PRO cc_start: 0.7037 (Cg_endo) cc_final: 0.6644 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6969 (ttm-80) cc_final: 0.6672 (ttm170) REVERT: A 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7606 (m-80) REVERT: A 309 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6959 (mm-30) REVERT: A 646 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7249 (mtm180) REVERT: A 704 SER cc_start: 0.8495 (p) cc_final: 0.8241 (m) REVERT: A 776 LYS cc_start: 0.6975 (tttt) cc_final: 0.6583 (ttpp) REVERT: A 817 PHE cc_start: 0.7387 (t80) cc_final: 0.6948 (t80) REVERT: A 868 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7110 (mp0) REVERT: A 950 ASP cc_start: 0.7786 (t70) cc_final: 0.7483 (m-30) REVERT: A 1045 LYS cc_start: 0.7708 (mtpp) cc_final: 0.7319 (mmtt) REVERT: B 271 GLN cc_start: 0.6076 (mt0) cc_final: 0.5770 (mm110) REVERT: B 390 LEU cc_start: 0.8113 (mt) cc_final: 0.7846 (mt) REVERT: B 507 PRO cc_start: 0.5851 (Cg_exo) cc_final: 0.5418 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6340 (m-80) cc_final: 0.5553 (m-80) REVERT: B 529 LYS cc_start: 0.7383 (mttm) cc_final: 0.7012 (mtmm) REVERT: B 646 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7118 (ttm170) REVERT: B 657 ASN cc_start: 0.7367 (t0) cc_final: 0.7014 (t0) REVERT: B 658 ASN cc_start: 0.6778 (m-40) cc_final: 0.6237 (t0) REVERT: B 702 GLU cc_start: 0.8314 (tt0) cc_final: 0.7753 (mm-30) REVERT: B 776 LYS cc_start: 0.7215 (tttt) cc_final: 0.6991 (tttm) REVERT: B 790 LYS cc_start: 0.7775 (ttpt) cc_final: 0.7449 (mmtt) REVERT: B 804 GLN cc_start: 0.8564 (mt0) cc_final: 0.8051 (mm110) REVERT: B 825 LYS cc_start: 0.6897 (mmtt) cc_final: 0.6450 (mtpt) REVERT: B 868 GLU cc_start: 0.7178 (pt0) cc_final: 0.6714 (mp0) REVERT: B 935 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6262 (mt0) REVERT: B 950 ASP cc_start: 0.6944 (t70) cc_final: 0.6627 (m-30) REVERT: B 954 GLN cc_start: 0.7684 (mt0) cc_final: 0.7481 (mt0) REVERT: B 960 ASN cc_start: 0.7447 (m-40) cc_final: 0.6836 (t0) REVERT: B 1038 LYS cc_start: 0.8227 (mttm) cc_final: 0.7865 (mmmt) REVERT: C 45 SER cc_start: 0.8236 (p) cc_final: 0.7750 (t) REVERT: C 140 PHE cc_start: 0.5665 (p90) cc_final: 0.5374 (p90) REVERT: C 224 GLU cc_start: 0.7510 (pm20) cc_final: 0.7232 (mt-10) REVERT: C 237 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7098 (mtm110) REVERT: C 427 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.5933 (t70) REVERT: C 508 TYR cc_start: 0.6346 (m-80) cc_final: 0.5809 (m-80) REVERT: C 606 ASN cc_start: 0.8394 (m-40) cc_final: 0.8160 (m-40) REVERT: C 646 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7213 (tpt90) REVERT: C 755 GLN cc_start: 0.7636 (mt0) cc_final: 0.7098 (mm110) REVERT: C 912 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 1038 LYS cc_start: 0.8056 (mttm) cc_final: 0.7496 (mmtp) REVERT: C 1045 LYS cc_start: 0.8451 (tttt) cc_final: 0.8194 (ttmt) REVERT: C 1081 ILE cc_start: 0.7409 (pt) cc_final: 0.7146 (pt) REVERT: F 34 MET cc_start: 0.2405 (mpp) cc_final: 0.1107 (ttp) REVERT: D 34 MET cc_start: 0.1997 (ptt) cc_final: 0.1786 (ptm) REVERT: E 34 MET cc_start: 0.4604 (mtm) cc_final: 0.4169 (mtm) outliers start: 62 outliers final: 53 residues processed: 301 average time/residue: 0.3754 time to fit residues: 180.8187 Evaluate side-chains 299 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 242 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 291 optimal weight: 4.9990 chunk 306 optimal weight: 20.0000 chunk 279 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 935 GLN C 957 GLN D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 27425 Z= 0.233 Angle : 0.534 9.522 37319 Z= 0.273 Chirality : 0.044 0.442 4431 Planarity : 0.003 0.041 4719 Dihedral : 5.404 55.822 4992 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.40 % Allowed : 10.69 % Favored : 86.91 % 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: 0.21 (0.14), residues: 3290 helix: 1.86 (0.21), residues: 633 sheet: 0.11 (0.17), residues: 856 loop : -0.43 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 PHE 0.020 0.001 PHE A 592 TYR 0.019 0.001 TYR E 95 ARG 0.008 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 248 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7554 (m-40) cc_final: 0.6997 (p0) REVERT: A 120 VAL cc_start: 0.6949 (t) cc_final: 0.6491 (p) REVERT: A 129 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6390 (ptpp) REVERT: A 230 PRO cc_start: 0.7165 (Cg_endo) cc_final: 0.6769 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6935 (ttm-80) cc_final: 0.6649 (ttm170) REVERT: A 269 TYR cc_start: 0.7905 (m-80) cc_final: 0.7612 (m-80) REVERT: A 309 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6991 (mm-30) REVERT: A 646 ARG cc_start: 0.7771 (tpp80) cc_final: 0.7259 (mtm180) REVERT: A 704 SER cc_start: 0.8428 (p) cc_final: 0.8186 (m) REVERT: A 776 LYS cc_start: 0.6976 (tttt) cc_final: 0.6583 (ttpp) REVERT: A 817 PHE cc_start: 0.7348 (t80) cc_final: 0.6911 (t80) REVERT: A 868 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7058 (mp0) REVERT: A 950 ASP cc_start: 0.7784 (t70) cc_final: 0.7485 (m-30) REVERT: A 1045 LYS cc_start: 0.7709 (mtpp) cc_final: 0.7319 (mmtt) REVERT: B 271 GLN cc_start: 0.6071 (mt0) cc_final: 0.5763 (mm110) REVERT: B 507 PRO cc_start: 0.5880 (Cg_exo) cc_final: 0.5462 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6315 (m-80) cc_final: 0.5530 (m-80) REVERT: B 529 LYS cc_start: 0.7366 (mttm) cc_final: 0.7004 (mtmm) REVERT: B 646 ARG cc_start: 0.7430 (tpp80) cc_final: 0.7127 (ttm170) REVERT: B 657 ASN cc_start: 0.7241 (t0) cc_final: 0.6938 (t0) REVERT: B 658 ASN cc_start: 0.6775 (m-40) cc_final: 0.6292 (t0) REVERT: B 702 GLU cc_start: 0.8291 (tt0) cc_final: 0.7716 (mm-30) REVERT: B 776 LYS cc_start: 0.7214 (tttt) cc_final: 0.6992 (tttm) REVERT: B 790 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7450 (mmtt) REVERT: B 804 GLN cc_start: 0.8680 (mt0) cc_final: 0.8069 (mm110) REVERT: B 825 LYS cc_start: 0.6896 (mmtt) cc_final: 0.6450 (mtpt) REVERT: B 868 GLU cc_start: 0.7090 (pt0) cc_final: 0.6650 (mp0) REVERT: B 935 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.6245 (mt0) REVERT: B 950 ASP cc_start: 0.6896 (t70) cc_final: 0.6593 (m-30) REVERT: B 954 GLN cc_start: 0.7731 (mt0) cc_final: 0.7515 (mt0) REVERT: B 960 ASN cc_start: 0.7441 (m-40) cc_final: 0.6844 (t0) REVERT: B 1038 LYS cc_start: 0.8229 (mttm) cc_final: 0.7866 (mmmt) REVERT: C 45 SER cc_start: 0.8246 (p) cc_final: 0.7756 (t) REVERT: C 140 PHE cc_start: 0.5556 (p90) cc_final: 0.5259 (p90) REVERT: C 224 GLU cc_start: 0.7615 (pm20) cc_final: 0.7320 (pm20) REVERT: C 237 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7062 (mtm110) REVERT: C 427 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.5939 (t70) REVERT: C 508 TYR cc_start: 0.6346 (m-80) cc_final: 0.5852 (m-80) REVERT: C 606 ASN cc_start: 0.8389 (m-40) cc_final: 0.8162 (m-40) REVERT: C 646 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7207 (tpt90) REVERT: C 755 GLN cc_start: 0.7640 (mt0) cc_final: 0.7102 (mm110) REVERT: C 912 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 1038 LYS cc_start: 0.8075 (mttm) cc_final: 0.7541 (mmtp) REVERT: C 1045 LYS cc_start: 0.8444 (tttt) cc_final: 0.8192 (ttmt) REVERT: C 1081 ILE cc_start: 0.7404 (pt) cc_final: 0.7144 (pt) REVERT: D 34 MET cc_start: 0.1748 (ptt) cc_final: 0.1305 (ptt) REVERT: E 34 MET cc_start: 0.4601 (mtm) cc_final: 0.4167 (mtm) outliers start: 64 outliers final: 58 residues processed: 296 average time/residue: 0.3858 time to fit residues: 183.5977 Evaluate side-chains 302 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 240 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 195 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 330 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 263 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27425 Z= 0.213 Angle : 0.522 9.515 37319 Z= 0.267 Chirality : 0.044 0.383 4431 Planarity : 0.003 0.042 4719 Dihedral : 5.208 55.790 4992 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.43 % Allowed : 10.80 % Favored : 86.77 % 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: 0.24 (0.14), residues: 3290 helix: 1.92 (0.21), residues: 633 sheet: 0.09 (0.17), residues: 832 loop : -0.39 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 436 HIS 0.006 0.001 HIS C 519 PHE 0.020 0.001 PHE A 592 TYR 0.019 0.001 TYR E 95 ARG 0.008 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6580 Ramachandran restraints generated. 3290 Oldfield, 0 Emsley, 3290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 246 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7591 (m-40) cc_final: 0.6881 (p0) REVERT: A 120 VAL cc_start: 0.6942 (t) cc_final: 0.6489 (p) REVERT: A 129 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6469 (ptpt) REVERT: A 230 PRO cc_start: 0.7222 (Cg_endo) cc_final: 0.6852 (Cg_exo) REVERT: A 237 ARG cc_start: 0.6869 (ttm-80) cc_final: 0.6596 (ttm170) REVERT: A 269 TYR cc_start: 0.7931 (m-80) cc_final: 0.7649 (m-80) REVERT: A 309 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7006 (mm-30) REVERT: A 646 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7290 (mtm180) REVERT: A 704 SER cc_start: 0.8429 (p) cc_final: 0.8187 (m) REVERT: A 776 LYS cc_start: 0.6975 (tttt) cc_final: 0.6582 (ttpp) REVERT: A 817 PHE cc_start: 0.7351 (t80) cc_final: 0.6886 (t80) REVERT: A 868 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7085 (mp0) REVERT: A 950 ASP cc_start: 0.7777 (t70) cc_final: 0.7483 (m-30) REVERT: A 1045 LYS cc_start: 0.7712 (mtpp) cc_final: 0.7323 (mmtt) REVERT: B 271 GLN cc_start: 0.6055 (mt0) cc_final: 0.5753 (mm110) REVERT: B 507 PRO cc_start: 0.5899 (Cg_exo) cc_final: 0.5484 (Cg_endo) REVERT: B 508 TYR cc_start: 0.6322 (m-80) cc_final: 0.5536 (m-80) REVERT: B 529 LYS cc_start: 0.7370 (mttm) cc_final: 0.6992 (mtmm) REVERT: B 646 ARG cc_start: 0.7421 (tpp80) cc_final: 0.7105 (mtp180) REVERT: B 658 ASN cc_start: 0.6866 (m-40) cc_final: 0.6298 (t0) REVERT: B 702 GLU cc_start: 0.8290 (tt0) cc_final: 0.7838 (mm-30) REVERT: B 776 LYS cc_start: 0.7218 (tttt) cc_final: 0.6999 (tttm) REVERT: B 790 LYS cc_start: 0.7773 (ttpt) cc_final: 0.7442 (mmmt) REVERT: B 804 GLN cc_start: 0.8666 (mt0) cc_final: 0.8061 (mm110) REVERT: B 825 LYS cc_start: 0.6863 (mmtt) cc_final: 0.6424 (mtpt) REVERT: B 868 GLU cc_start: 0.7085 (pt0) cc_final: 0.6649 (mp0) REVERT: B 935 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6236 (mt0) REVERT: B 950 ASP cc_start: 0.6892 (t70) cc_final: 0.6589 (m-30) REVERT: B 954 GLN cc_start: 0.7735 (mt0) cc_final: 0.7518 (mt0) REVERT: B 960 ASN cc_start: 0.7438 (m-40) cc_final: 0.6818 (t0) REVERT: B 1038 LYS cc_start: 0.8227 (mttm) cc_final: 0.7864 (mmmt) REVERT: C 224 GLU cc_start: 0.7522 (pm20) cc_final: 0.7245 (mt-10) REVERT: C 237 ARG cc_start: 0.7562 (mtt180) cc_final: 0.7080 (mtm110) REVERT: C 427 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.5972 (t70) REVERT: C 508 TYR cc_start: 0.6345 (m-80) cc_final: 0.5895 (m-80) REVERT: C 606 ASN cc_start: 0.8384 (m-40) cc_final: 0.8155 (m-40) REVERT: C 646 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7171 (tpt90) REVERT: C 755 GLN cc_start: 0.7638 (mt0) cc_final: 0.7101 (mm110) REVERT: C 912 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7988 (p) REVERT: C 1038 LYS cc_start: 0.8067 (mttm) cc_final: 0.7562 (mmtp) REVERT: C 1045 LYS cc_start: 0.8450 (tttt) cc_final: 0.8200 (ttmt) REVERT: C 1081 ILE cc_start: 0.7389 (pt) cc_final: 0.7126 (pt) REVERT: F 34 MET cc_start: 0.2312 (mpp) cc_final: 0.0933 (ttp) REVERT: D 12 MET cc_start: -0.1280 (ptp) cc_final: -0.1491 (ppp) REVERT: D 34 MET cc_start: 0.1598 (ptt) cc_final: 0.1270 (ptt) REVERT: E 34 MET cc_start: 0.4570 (mtm) cc_final: 0.4148 (mtm) outliers start: 64 outliers final: 59 residues processed: 297 average time/residue: 0.4143 time to fit residues: 199.3060 Evaluate side-chains 301 residues out of total 2887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 209 optimal weight: 6.9990 chunk 280 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 270 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.204175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.161303 restraints weight = 55129.824| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.84 r_work: 0.3173 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27425 Z= 0.171 Angle : 0.499 9.514 37319 Z= 0.256 Chirality : 0.044 0.492 4431 Planarity : 0.003 0.044 4719 Dihedral : 4.945 55.715 4992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.29 % Allowed : 11.04 % Favored : 86.66 % 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: 0.31 (0.14), residues: 3290 helix: 2.02 (0.21), residues: 634 sheet: 0.08 (0.17), residues: 867 loop : -0.35 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 436 HIS 0.005 0.001 HIS C 519 PHE 0.020 0.001 PHE A 643 TYR 0.018 0.001 TYR E 95 ARG 0.008 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5566.98 seconds wall clock time: 101 minutes 20.85 seconds (6080.85 seconds total)