Starting phenix.real_space_refine on Wed Feb 21 09:14:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h00_34407/02_2024/8h00_34407.pdb" } resolution = 3.41 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= -0.001 sd= 0.044 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 141 5.16 5 C 19242 2.51 5 N 4940 2.21 5 O 5858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 102": "OD1" <-> "OD2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G ASP 102": "OD1" <-> "OD2" Residue "H ASP 96": "OD1" <-> "OD2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30181 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8121 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} 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: "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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 16.15, per 1000 atoms: 0.54 Number of scatterers: 30181 At special positions: 0 Unit cell: (146.432, 153.92, 196.352, 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 141 16.00 O 5858 8.00 N 4940 7.00 C 19242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 50 " 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 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 12.37 Conformation dependent library (CDL) restraints added in 5.3 seconds 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 62 sheets defined 20.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.718A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) 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 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.142A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.595A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.228A 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 945 through 965 removed outlier: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.237A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.266A 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 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.904A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.549A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.534A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.233A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.683A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.645A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.036A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.431A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.931A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.867A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.572A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.732A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.671A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.561A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.110A 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 945 through 966 removed outlier: 3.580A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.235A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.613A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.608A pdb=" N LYS E 66 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.914A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.630A pdb=" N LYS G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.602A pdb=" N LYS I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.878A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.533A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A 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: 5.169A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.578A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.833A 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: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.199A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.972A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.593A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.087A 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 539 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.528A 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: 4.520A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.499A 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 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.323A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.514A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.703A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.282A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.807A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.976A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.776A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.616A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.808A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.062A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.395A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.617A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.183A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.910A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.350A pdb=" N VAL D 11 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 105 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.627A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.340A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.570A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.471A pdb=" N VAL F 11 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS F 110 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU F 13 " --> pdb=" O LYS F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.781A pdb=" N MET G 83 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.886A pdb=" N LEU G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 60 through 61 removed outlier: 4.249A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 51 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.511A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.378A pdb=" N VAL H 11 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 105 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.525A pdb=" N THR I 20 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.372A pdb=" N MET I 34 " --> pdb=" O CYS I 50 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.43 Time building geometry restraints manager: 13.31 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: 9551 1.34 - 1.46: 7701 1.46 - 1.59: 13448 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30877 Sorted by residual: bond pdb=" N VAL A1033 " pdb=" CA VAL A1033 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" N GLN F 70 " pdb=" CA GLN F 70 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.10e+00 bond pdb=" N GLY A1035 " pdb=" CA GLY A1035 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.19e-02 7.06e+03 7.62e+00 bond pdb=" N GLN F 38 " pdb=" CA GLN F 38 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.78e+00 bond pdb=" N LEU A1034 " pdb=" CA LEU A1034 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.66e+00 ... (remaining 30872 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.57: 653 105.57 - 112.70: 16508 112.70 - 119.82: 9523 119.82 - 126.94: 15007 126.94 - 134.07: 323 Bond angle restraints: 42014 Sorted by residual: angle pdb=" N GLU B 516 " pdb=" CA GLU B 516 " pdb=" C GLU B 516 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA GLY A1035 " pdb=" C GLY A1035 " pdb=" O GLY A1035 " ideal model delta sigma weight residual 121.38 118.23 3.15 9.40e-01 1.13e+00 1.12e+01 angle pdb=" N ARG C 102 " pdb=" CA ARG C 102 " pdb=" C ARG C 102 " ideal model delta sigma weight residual 113.88 110.10 3.78 1.23e+00 6.61e-01 9.43e+00 angle pdb=" N SER I 6 " pdb=" CA SER I 6 " pdb=" C SER I 6 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.94e+00 angle pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " ideal model delta sigma weight residual 112.00 118.51 -6.51 2.20e+00 2.07e-01 8.77e+00 ... (remaining 42009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17282 17.92 - 35.84: 1331 35.84 - 53.76: 238 53.76 - 71.68: 59 71.68 - 89.60: 35 Dihedral angle restraints: 18945 sinusoidal: 7926 harmonic: 11019 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.80 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 33.41 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 33.61 59.39 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 18942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4016 0.057 - 0.113: 782 0.113 - 0.170: 80 0.170 - 0.227: 1 0.227 - 0.283: 4 Chirality restraints: 4883 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4880 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 112 " -0.017 2.00e-02 2.50e+03 1.80e-02 8.10e+00 pdb=" CG TRP G 112 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP G 112 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 112 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP G 112 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO C 987 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 986 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.029 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1738 2.73 - 3.27: 29664 3.27 - 3.81: 47931 3.81 - 4.36: 56474 4.36 - 4.90: 100762 Nonbonded interactions: 236569 Sorted by model distance: nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.184 2.520 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.207 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.211 2.440 nonbonded pdb=" OE1 GLN C 992 " pdb=" NH2 ARG C 995 " model vdw 2.222 2.520 ... (remaining 236564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 28.820 Check model and map are aligned: 0.510 Set scattering table: 0.270 Process input model: 83.360 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.470 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: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.005 0.052 30877 Z= 0.299 Angle : 0.606 7.514 42014 Z= 0.326 Chirality : 0.046 0.283 4883 Planarity : 0.004 0.058 5354 Dihedral : 13.254 89.605 11714 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.13), residues: 3737 helix: 1.87 (0.21), residues: 651 sheet: 0.08 (0.17), residues: 915 loop : -0.88 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 112 HIS 0.004 0.001 HIS B1058 PHE 0.032 0.002 PHE C 823 TYR 0.033 0.001 TYR C 904 ARG 0.013 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8304 (ptm) cc_final: 0.8026 (ptm) REVERT: B 368 LEU cc_start: 0.8858 (mt) cc_final: 0.8099 (tp) REVERT: E 11 VAL cc_start: 0.7489 (t) cc_final: 0.7121 (m) REVERT: E 34 MET cc_start: 0.7986 (tpp) cc_final: 0.7599 (tpp) REVERT: E 71 ILE cc_start: 0.8027 (tt) cc_final: 0.7800 (tt) REVERT: F 76 ASN cc_start: 0.8387 (m-40) cc_final: 0.7892 (p0) REVERT: F 106 GLU cc_start: 0.8611 (pm20) cc_final: 0.8305 (pm20) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.4039 time to fit residues: 172.2780 Evaluate side-chains 183 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 37 GLN F 70 GLN H 31 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30877 Z= 0.193 Angle : 0.532 9.619 42014 Z= 0.279 Chirality : 0.044 0.294 4883 Planarity : 0.004 0.065 5354 Dihedral : 6.248 57.928 5012 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 0.55 % Allowed : 5.30 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.05 (0.13), residues: 3737 helix: 1.92 (0.21), residues: 666 sheet: 0.35 (0.17), residues: 932 loop : -0.87 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 112 HIS 0.003 0.001 HIS B 519 PHE 0.027 0.001 PHE A 374 TYR 0.026 0.001 TYR B 756 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 3.741 Fit side-chains revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7713 (m-80) cc_final: 0.7485 (m-80) REVERT: B 368 LEU cc_start: 0.8859 (mt) cc_final: 0.8242 (tp) REVERT: E 71 ILE cc_start: 0.7958 (tt) cc_final: 0.7726 (tt) REVERT: F 76 ASN cc_start: 0.8302 (m-40) cc_final: 0.7978 (p0) REVERT: F 106 GLU cc_start: 0.8585 (pm20) cc_final: 0.8244 (pm20) REVERT: G 34 MET cc_start: 0.7349 (tpp) cc_final: 0.7109 (tpp) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 0.3691 time to fit residues: 135.1419 Evaluate side-chains 188 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain I residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 285 optimal weight: 0.5980 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 343 optimal weight: 9.9990 chunk 371 optimal weight: 0.9990 chunk 306 optimal weight: 0.0980 chunk 341 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C1142 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30877 Z= 0.154 Angle : 0.491 9.745 42014 Z= 0.255 Chirality : 0.043 0.298 4883 Planarity : 0.004 0.060 5354 Dihedral : 5.603 55.704 5012 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 0.73 % Allowed : 7.34 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.05 (0.14), residues: 3737 helix: 2.06 (0.21), residues: 669 sheet: 0.48 (0.17), residues: 925 loop : -0.85 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 112 HIS 0.003 0.001 HIS B 519 PHE 0.039 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.009 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7680 (m-80) cc_final: 0.7437 (m-80) REVERT: B 368 LEU cc_start: 0.8872 (mt) cc_final: 0.8279 (tp) REVERT: C 950 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7362 (m-30) REVERT: F 106 GLU cc_start: 0.8589 (pm20) cc_final: 0.8212 (pm20) outliers start: 24 outliers final: 17 residues processed: 211 average time/residue: 0.3686 time to fit residues: 134.2477 Evaluate side-chains 197 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 178 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 chunk 345 optimal weight: 9.9990 chunk 365 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 245 HIS ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 853 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30877 Z= 0.469 Angle : 0.625 9.848 42014 Z= 0.324 Chirality : 0.047 0.300 4883 Planarity : 0.004 0.059 5354 Dihedral : 5.643 54.903 5012 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.34 % Allowed : 10.05 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.26 (0.13), residues: 3737 helix: 1.73 (0.21), residues: 668 sheet: 0.21 (0.16), residues: 973 loop : -1.01 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 112 HIS 0.007 0.002 HIS A1058 PHE 0.032 0.002 PHE C 559 TYR 0.019 0.002 TYR C1067 ARG 0.005 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ASN cc_start: 0.8457 (t0) cc_final: 0.8211 (t0) REVERT: B 200 TYR cc_start: 0.7816 (m-80) cc_final: 0.7596 (m-80) REVERT: B 368 LEU cc_start: 0.8911 (mt) cc_final: 0.8272 (tp) REVERT: C 314 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7342 (tm-30) REVERT: G 34 MET cc_start: 0.7592 (tpp) cc_final: 0.7352 (tpp) outliers start: 44 outliers final: 31 residues processed: 223 average time/residue: 0.3807 time to fit residues: 144.0504 Evaluate side-chains 205 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 3.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 272 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 311 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 327 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30877 Z= 0.167 Angle : 0.507 10.588 42014 Z= 0.262 Chirality : 0.043 0.266 4883 Planarity : 0.004 0.057 5354 Dihedral : 5.225 56.098 5012 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.27 % Rotamer: Outliers : 1.37 % Allowed : 10.93 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.02 (0.14), residues: 3737 helix: 2.07 (0.21), residues: 659 sheet: 0.40 (0.16), residues: 970 loop : -0.92 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.004 0.000 HIS B 207 PHE 0.038 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 368 LEU cc_start: 0.8917 (mt) cc_final: 0.8296 (tp) REVERT: C 950 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: F 106 GLU cc_start: 0.8584 (pm20) cc_final: 0.8281 (pm20) outliers start: 45 outliers final: 29 residues processed: 220 average time/residue: 0.3660 time to fit residues: 138.0064 Evaluate side-chains 201 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 0.6980 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 365 optimal weight: 6.9990 chunk 303 optimal weight: 0.0980 chunk 169 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30877 Z= 0.283 Angle : 0.540 10.725 42014 Z= 0.278 Chirality : 0.044 0.273 4883 Planarity : 0.004 0.056 5354 Dihedral : 5.161 55.079 5012 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 1.58 % Allowed : 11.87 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.13 (0.14), residues: 3737 helix: 1.94 (0.21), residues: 674 sheet: 0.22 (0.16), residues: 971 loop : -0.94 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A1058 PHE 0.023 0.001 PHE C 559 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 178 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 368 LEU cc_start: 0.8909 (mt) cc_final: 0.8338 (tp) REVERT: B 1029 MET cc_start: 0.8874 (tpp) cc_final: 0.8583 (ttm) REVERT: C 950 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: F 106 GLU cc_start: 0.8568 (pm20) cc_final: 0.8237 (pm20) REVERT: G 34 MET cc_start: 0.7554 (tpp) cc_final: 0.7345 (tpp) outliers start: 52 outliers final: 41 residues processed: 218 average time/residue: 0.3896 time to fit residues: 148.0392 Evaluate side-chains 215 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 208 optimal weight: 4.9990 chunk 267 optimal weight: 0.0870 chunk 206 optimal weight: 20.0000 chunk 307 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 222 optimal weight: 0.0060 chunk 168 optimal weight: 8.9990 overall best weight: 1.0976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30877 Z= 0.202 Angle : 0.520 11.373 42014 Z= 0.267 Chirality : 0.044 0.263 4883 Planarity : 0.004 0.071 5354 Dihedral : 5.044 55.446 5012 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 1.70 % Allowed : 12.30 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.06 (0.14), residues: 3737 helix: 2.03 (0.21), residues: 674 sheet: 0.29 (0.17), residues: 954 loop : -0.91 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS B 207 PHE 0.042 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 368 LEU cc_start: 0.8925 (mt) cc_final: 0.8334 (tp) REVERT: C 950 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: F 106 GLU cc_start: 0.8576 (pm20) cc_final: 0.8237 (pm20) REVERT: G 5 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6194 (mp0) REVERT: G 34 MET cc_start: 0.7593 (tpp) cc_final: 0.7388 (tpp) outliers start: 56 outliers final: 47 residues processed: 220 average time/residue: 0.3834 time to fit residues: 144.8636 Evaluate side-chains 219 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 217 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.0270 chunk 231 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30877 Z= 0.162 Angle : 0.508 11.575 42014 Z= 0.260 Chirality : 0.043 0.251 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.874 55.313 5012 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 1.55 % Allowed : 12.75 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.03 (0.14), residues: 3737 helix: 2.24 (0.21), residues: 662 sheet: 0.34 (0.17), residues: 954 loop : -0.88 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS B 207 PHE 0.040 0.001 PHE B 374 TYR 0.019 0.001 TYR C1067 ARG 0.008 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 177 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 368 LEU cc_start: 0.8926 (mt) cc_final: 0.8391 (tp) REVERT: C 950 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: F 106 GLU cc_start: 0.8566 (pm20) cc_final: 0.8236 (pm20) REVERT: G 5 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6226 (mp0) REVERT: G 34 MET cc_start: 0.7519 (tpp) cc_final: 0.7301 (tpp) outliers start: 51 outliers final: 45 residues processed: 214 average time/residue: 0.3749 time to fit residues: 139.0842 Evaluate side-chains 221 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 318 optimal weight: 0.4980 chunk 339 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 306 optimal weight: 0.0470 chunk 321 optimal weight: 5.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30877 Z= 0.276 Angle : 0.543 11.455 42014 Z= 0.278 Chirality : 0.044 0.269 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.910 55.013 5012 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.70 % Allowed : 12.79 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.06 (0.14), residues: 3737 helix: 2.15 (0.21), residues: 662 sheet: 0.28 (0.17), residues: 951 loop : -0.93 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS A1058 PHE 0.040 0.001 PHE B 374 TYR 0.028 0.001 TYR C 904 ARG 0.006 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ASN cc_start: 0.8489 (t0) cc_final: 0.8188 (t0) REVERT: B 368 LEU cc_start: 0.8929 (mt) cc_final: 0.8360 (tp) REVERT: C 950 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: F 106 GLU cc_start: 0.8562 (pm20) cc_final: 0.8230 (pm20) outliers start: 56 outliers final: 47 residues processed: 213 average time/residue: 0.3544 time to fit residues: 131.1354 Evaluate side-chains 219 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 376 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 299 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30877 Z= 0.316 Angle : 0.570 12.416 42014 Z= 0.292 Chirality : 0.045 0.282 4883 Planarity : 0.004 0.067 5354 Dihedral : 5.017 55.177 5012 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.58 % Allowed : 13.06 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.14 (0.14), residues: 3737 helix: 2.11 (0.21), residues: 662 sheet: 0.18 (0.17), residues: 948 loop : -0.97 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 36 HIS 0.004 0.001 HIS A1058 PHE 0.038 0.001 PHE B 374 TYR 0.024 0.001 TYR B 904 ARG 0.008 0.000 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 137 ASN cc_start: 0.8498 (t0) cc_final: 0.8198 (t0) REVERT: B 368 LEU cc_start: 0.8934 (mt) cc_final: 0.8400 (tp) REVERT: C 950 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7413 (m-30) REVERT: D 4 MET cc_start: 0.7601 (mmt) cc_final: 0.7277 (mmt) REVERT: F 106 GLU cc_start: 0.8528 (pm20) cc_final: 0.8208 (pm20) outliers start: 52 outliers final: 47 residues processed: 212 average time/residue: 0.3636 time to fit residues: 133.4850 Evaluate side-chains 220 residues out of total 3285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 319 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 276 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 308 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063348 restraints weight = 75500.756| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.30 r_work: 0.2880 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30877 Z= 0.174 Angle : 0.520 12.593 42014 Z= 0.265 Chirality : 0.043 0.262 4883 Planarity : 0.004 0.066 5354 Dihedral : 4.816 55.465 5012 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 13.27 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.01 (0.14), residues: 3737 helix: 2.27 (0.21), residues: 662 sheet: 0.25 (0.17), residues: 958 loop : -0.90 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 36 HIS 0.003 0.001 HIS B 207 PHE 0.040 0.001 PHE B 374 TYR 0.023 0.001 TYR B 904 ARG 0.008 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5551.70 seconds wall clock time: 104 minutes 12.24 seconds (6252.24 seconds total)