Starting phenix.real_space_refine on Thu Feb 22 14:29:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q6e_13857/02_2024/7q6e_13857.pdb" } resolution = 2.7 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= 0.002 sd= 0.034 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 144 5.16 5 C 21773 2.51 5 N 5619 2.21 5 O 6805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "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: 34341 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7903 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 51, 'TRANS': 961} Chain breaks: 7 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "C" Number of atoms: 7811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 51, 'TRANS': 949} Chain breaks: 7 Chain: "L" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.64, per 1000 atoms: 0.48 Number of scatterers: 34341 At special positions: 0 Unit cell: (162.36, 166.46, 214.02, 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 144 16.00 O 6805 8.00 N 5619 7.00 C 21773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 136 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN P 4 " - " MAN P 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA V 3 " - " MAN V 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 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 P 2 " - " BMA P 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG D 1 " - " FUC D 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " " NAG V 1 " - " FUC V 7 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 714 " " NAG M 1 " - " ASN A 798 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 714 " " NAG S 1 " - " ASN B 798 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 340 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1095 " " NAG Z 1 " - " ASN C1131 " Time building additional restraints: 14.32 Conformation dependent library (CDL) restraints added in 6.5 seconds 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8052 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 82 sheets defined 20.7% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.256A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.623A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.351A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.511A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.612A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.077A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.270A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.200A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.761A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.161A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.582A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.899A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.635A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.057A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.965A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.536A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.609A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.908A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.013A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.743A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.334A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.825A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.713A pdb=" N SER L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.712A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.013A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 removed outlier: 3.525A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.568A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 185 through 190 removed outlier: 3.550A pdb=" N LYS K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 192 through 194 No H-bonds generated for 'chain 'J' and resid 192 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.832A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.900A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.522A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 140 removed outlier: 3.608A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.972A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.101A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.618A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.277A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701 removed outlier: 3.549A pdb=" N LYS B 787 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.808A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A1103 " --> pdb=" O GLU A1108 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A1108 " --> pdb=" O GLN A1103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.009A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.448A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.819A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.842A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.605A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.518A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 140 removed outlier: 6.302A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.329A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.779A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.779A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.620A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.705A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.878A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AD5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.763A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.027A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.405A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.602A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.075A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.530A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.013A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.488A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.717A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.760A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.377A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.801A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.036A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.394A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.619A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.571A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.938A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.442A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 198 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.925A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.925A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.408A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.682A pdb=" N TYR F 88 " --> pdb=" O TYR F 37 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'F' and resid 116 through 120 removed outlier: 5.660A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 156 through 157 removed outlier: 4.678A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 209 " --> pdb=" O CYS F 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.683A pdb=" N GLU E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.683A pdb=" N GLU E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.880A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.880A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 182 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.287A pdb=" N TYR E 199 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.532A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AI3, first strand: chain 'K' and resid 116 through 120 removed outlier: 3.620A pdb=" N VAL K 135 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER K 133 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU K 183 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL K 135 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU K 181 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU K 137 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER K 179 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN K 139 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU K 177 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 156 through 157 removed outlier: 4.668A pdb=" N TRP K 150 " --> pdb=" O GLN K 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.590A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.790A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.790A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 125 through 129 removed outlier: 3.910A pdb=" N GLY J 144 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 186 " --> pdb=" O HIS J 169 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 125 through 129 removed outlier: 3.910A pdb=" N GLY J 144 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR J 199 " --> pdb=" O VAL J 216 " (cutoff:3.500A) 1503 hydrogen bonds defined for protein. 3981 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: 19.01 Time building geometry restraints manager: 15.19 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: 10862 1.34 - 1.46: 8828 1.46 - 1.58: 15229 1.58 - 1.70: 2 1.70 - 1.82: 180 Bond restraints: 35101 Sorted by residual: bond pdb=" C1 MAN P 5 " pdb=" C2 MAN P 5 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 MAN P 5 " pdb=" O5 MAN P 5 " ideal model delta sigma weight residual 1.399 1.467 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C2 MAN V 4 " pdb=" O2 MAN V 4 " ideal model delta sigma weight residual 1.407 1.453 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" C2 MAN V 4 " pdb=" C3 MAN V 4 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 35096 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 1045 106.58 - 113.44: 19605 113.44 - 120.30: 11858 120.30 - 127.15: 14908 127.15 - 134.01: 354 Bond angle restraints: 47770 Sorted by residual: angle pdb=" N ALA F 52 " pdb=" CA ALA F 52 " pdb=" CB ALA F 52 " ideal model delta sigma weight residual 114.17 110.27 3.90 1.14e+00 7.69e-01 1.17e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.75 110.60 4.15 1.26e+00 6.30e-01 1.08e+01 angle pdb=" N THR B 520 " pdb=" CA THR B 520 " pdb=" C THR B 520 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.48e+00 angle pdb=" CA VAL E 189 " pdb=" C VAL E 189 " pdb=" N PRO E 190 " ideal model delta sigma weight residual 117.00 119.36 -2.36 9.50e-01 1.11e+00 6.15e+00 angle pdb=" CA GLY A 473 " pdb=" C GLY A 473 " pdb=" N SER A 474 " ideal model delta sigma weight residual 114.65 116.87 -2.22 9.20e-01 1.18e+00 5.85e+00 ... (remaining 47765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 21149 21.63 - 43.26: 571 43.26 - 64.89: 111 64.89 - 86.52: 31 86.52 - 108.15: 18 Dihedral angle restraints: 21880 sinusoidal: 9346 harmonic: 12534 Sorted by residual: dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.28 47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.14 47.14 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 21877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4767 0.055 - 0.111: 724 0.111 - 0.166: 170 0.166 - 0.221: 1 0.221 - 0.277: 3 Chirality restraints: 5665 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5662 not shown) Planarity restraints: 6092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO H 154 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 154 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 153 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO J 154 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 6089 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 662 2.68 - 3.24: 32132 3.24 - 3.79: 52843 3.79 - 4.35: 75441 4.35 - 4.90: 124005 Nonbonded interactions: 285083 Sorted by model distance: nonbonded pdb=" NH1 ARG A1088 " pdb=" O THR A1117 " model vdw 2.127 2.520 nonbonded pdb=" O THR J 28 " pdb=" OG SER J 32 " model vdw 2.191 2.440 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.191 2.440 nonbonded pdb=" OG SER E 30 " pdb=" OE2 GLU E 74 " model vdw 2.206 2.440 nonbonded pdb=" OG SER H 30 " pdb=" OE2 GLU H 74 " model vdw 2.209 2.440 ... (remaining 285078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 143 or resid 165 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1308)) selection = (chain 'B' and (resid 22 through 143 or resid 165 through 1144 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 22 through 617 or resid 638 through 1144 or resid 1301 thr \ ough 1308)) } ncs_group { reference = (chain 'D' and (resid 2 or resid 5 through 7)) selection = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'V' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 17.030 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 95.150 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.510 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 35101 Z= 0.228 Angle : 0.541 7.214 47770 Z= 0.269 Chirality : 0.045 0.277 5665 Planarity : 0.003 0.046 6049 Dihedral : 10.950 108.148 13675 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.48 % Allowed : 3.21 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.33 (0.13), residues: 4267 helix: 1.04 (0.20), residues: 731 sheet: 0.46 (0.14), residues: 1259 loop : -0.10 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 883 HIS 0.002 0.001 HIS A1061 PHE 0.011 0.001 PHE C 756 TYR 0.015 0.001 TYR C1064 ARG 0.003 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 558 time to evaluate : 3.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.6610 (mt) cc_final: 0.6397 (mt) REVERT: A 449 LEU cc_start: 0.8376 (mt) cc_final: 0.8097 (mt) REVERT: A 787 LYS cc_start: 0.8388 (ptmt) cc_final: 0.7813 (mmpt) REVERT: A 926 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 129 LYS cc_start: 0.7605 (mttt) cc_final: 0.7205 (mmpt) REVERT: B 207 HIS cc_start: 0.7762 (m170) cc_final: 0.7513 (m-70) REVERT: B 239 GLN cc_start: 0.6894 (tt0) cc_final: 0.6551 (tm-30) REVERT: B 375 LYS cc_start: 0.8245 (mttt) cc_final: 0.7559 (mtmt) REVERT: B 526 LYS cc_start: 0.8807 (mttt) cc_final: 0.8508 (mmpt) REVERT: L 80 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6648 (mp0) REVERT: F 80 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6452 (mm-30) REVERT: E 23 LYS cc_start: 0.8613 (mttt) cc_final: 0.7749 (mtpm) REVERT: K 55 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7864 (mtm-85) REVERT: K 168 GLN cc_start: 0.7483 (tt0) cc_final: 0.6199 (tt0) REVERT: J 23 LYS cc_start: 0.8888 (mttp) cc_final: 0.8668 (mttp) REVERT: J 81 MET cc_start: 0.8034 (tmm) cc_final: 0.7723 (tmm) REVERT: J 180 LEU cc_start: 0.8563 (mt) cc_final: 0.8343 (tt) outliers start: 18 outliers final: 11 residues processed: 574 average time/residue: 1.5211 time to fit residues: 1037.1531 Evaluate side-chains 371 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 359 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 50.0000 chunk 323 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 334 optimal weight: 30.0000 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A1007 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS B 776 GLN B 951 GLN B1116 ASN C 391 ASN C 490 GLN C 748 ASN C 954 GLN C 966 ASN L 139 ASN H 59 ASN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN K 38 GLN K 39 GLN J 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 35101 Z= 0.466 Angle : 0.638 9.805 47770 Z= 0.331 Chirality : 0.050 0.391 5665 Planarity : 0.005 0.055 6049 Dihedral : 8.390 91.483 6159 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.38 % Allowed : 8.85 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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: 0.25 (0.13), residues: 4267 helix: 0.93 (0.19), residues: 731 sheet: 0.51 (0.14), residues: 1293 loop : -0.21 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 433 HIS 0.008 0.001 HIS C1061 PHE 0.016 0.002 PHE C 426 TYR 0.024 0.002 TYR C 393 ARG 0.010 0.001 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 363 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: A 311 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: A 449 LEU cc_start: 0.8370 (mt) cc_final: 0.8086 (mt) REVERT: A 805 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: A 954 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7409 (tp40) REVERT: B 129 LYS cc_start: 0.7690 (mttt) cc_final: 0.7209 (mmpt) REVERT: B 239 GLN cc_start: 0.7353 (tt0) cc_final: 0.7075 (pp30) REVERT: B 375 LYS cc_start: 0.8255 (mttt) cc_final: 0.7565 (mtmt) REVERT: B 526 LYS cc_start: 0.8809 (mttt) cc_final: 0.8425 (mmtt) REVERT: B 1089 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: B 1141 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8443 (mm-30) REVERT: C 985 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7340 (tm-30) REVERT: L 27 GLN cc_start: 0.8136 (mt0) cc_final: 0.7910 (mt0) REVERT: L 80 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6633 (mp0) REVERT: L 109 LYS cc_start: 0.8193 (tppp) cc_final: 0.7987 (tppp) REVERT: L 189 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7934 (mp0) REVERT: H 3 GLN cc_start: 0.8139 (tt0) cc_final: 0.7938 (tt0) REVERT: H 180 LEU cc_start: 0.8914 (mm) cc_final: 0.8654 (tp) REVERT: F 107 GLU cc_start: 0.7386 (pt0) cc_final: 0.6885 (tt0) REVERT: E 23 LYS cc_start: 0.8633 (mttt) cc_final: 0.7752 (mtpm) REVERT: K 55 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7928 (mtm-85) REVERT: K 94 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8467 (p) REVERT: J 67 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7307 (mtm110) REVERT: J 180 LEU cc_start: 0.8617 (mt) cc_final: 0.8346 (tt) outliers start: 89 outliers final: 50 residues processed: 421 average time/residue: 1.5482 time to fit residues: 780.2901 Evaluate side-chains 383 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 326 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 67 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 0.6980 chunk 264 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 388 optimal weight: 0.5980 chunk 419 optimal weight: 50.0000 chunk 345 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 610 GLN A 752 GLN B 196 ASN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN B 952 ASN C 954 GLN C 999 GLN C1007 GLN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35101 Z= 0.291 Angle : 0.563 10.098 47770 Z= 0.290 Chirality : 0.046 0.377 5665 Planarity : 0.004 0.045 6049 Dihedral : 7.560 75.863 6152 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.43 % Allowed : 10.35 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.39 (0.13), residues: 4267 helix: 1.28 (0.20), residues: 727 sheet: 0.53 (0.14), residues: 1300 loop : -0.18 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 150 HIS 0.005 0.001 HIS B 207 PHE 0.016 0.002 PHE B 397 TYR 0.022 0.001 TYR A 366 ARG 0.008 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 337 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 268 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: A 311 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 449 LEU cc_start: 0.8364 (mt) cc_final: 0.8057 (mt) REVERT: A 805 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6657 (m-30) REVERT: A 918 LYS cc_start: 0.8481 (mmpt) cc_final: 0.8245 (mmpt) REVERT: A 954 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7395 (tp40) REVERT: B 129 LYS cc_start: 0.7682 (mttt) cc_final: 0.7190 (mmpt) REVERT: B 375 LYS cc_start: 0.8234 (mttt) cc_final: 0.7553 (mtmt) REVERT: B 526 LYS cc_start: 0.8820 (mttt) cc_final: 0.8474 (mmtt) REVERT: B 574 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7238 (ttm110) REVERT: B 658 GLU cc_start: 0.7791 (tt0) cc_final: 0.7487 (tt0) REVERT: B 1089 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6545 (mp0) REVERT: C 487 PHE cc_start: 0.7310 (t80) cc_final: 0.7086 (t80) REVERT: L 27 GLN cc_start: 0.8091 (mt0) cc_final: 0.7877 (mt0) REVERT: L 80 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6610 (mp0) REVERT: H 82 GLU cc_start: 0.7821 (tt0) cc_final: 0.7593 (tt0) REVERT: H 180 LEU cc_start: 0.8890 (mm) cc_final: 0.8638 (tp) REVERT: F 107 GLU cc_start: 0.7411 (pt0) cc_final: 0.6888 (tt0) REVERT: E 81 MET cc_start: 0.8615 (ttp) cc_final: 0.8349 (ttp) REVERT: E 183 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7650 (mp) REVERT: K 55 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7948 (mtm-85) REVERT: J 38 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7271 (ttt180) REVERT: J 67 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7297 (mtm110) REVERT: J 180 LEU cc_start: 0.8569 (mt) cc_final: 0.8251 (tt) outliers start: 91 outliers final: 50 residues processed: 391 average time/residue: 1.5228 time to fit residues: 709.6213 Evaluate side-chains 378 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 318 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 0.0470 chunk 292 optimal weight: 0.9990 chunk 201 optimal weight: 10.0000 chunk 42 optimal weight: 0.0040 chunk 185 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 389 optimal weight: 0.3980 chunk 412 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 369 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 610 GLN A 752 GLN B 196 ASN B 239 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B1098 HIS B1103 GLN C 954 GLN C 999 GLN H 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35101 Z= 0.145 Angle : 0.509 10.892 47770 Z= 0.259 Chirality : 0.044 0.378 5665 Planarity : 0.004 0.045 6049 Dihedral : 6.680 68.364 6152 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.33 % Allowed : 10.81 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.61 (0.13), residues: 4267 helix: 1.67 (0.20), residues: 734 sheet: 0.62 (0.14), residues: 1311 loop : -0.08 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 150 HIS 0.005 0.001 HIS B 207 PHE 0.020 0.001 PHE B 397 TYR 0.023 0.001 TYR C 366 ARG 0.011 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 348 time to evaluate : 3.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 63 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7171 (p) REVERT: A 268 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: A 311 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: A 449 LEU cc_start: 0.8379 (mt) cc_final: 0.8058 (mt) REVERT: A 787 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7403 (mmpt) REVERT: A 805 ASP cc_start: 0.7278 (m-30) cc_final: 0.6647 (m-30) REVERT: A 954 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7390 (tp40) REVERT: A 1007 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7126 (mp10) REVERT: B 129 LYS cc_start: 0.7670 (mttt) cc_final: 0.7190 (mmpt) REVERT: B 237 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7348 (mtm110) REVERT: B 239 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: B 375 LYS cc_start: 0.8263 (mttt) cc_final: 0.7569 (mtmt) REVERT: B 526 LYS cc_start: 0.8816 (mttt) cc_final: 0.8485 (mmtt) REVERT: B 574 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7069 (ttm110) REVERT: B 658 GLU cc_start: 0.7715 (tt0) cc_final: 0.7397 (tt0) REVERT: B 1002 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7631 (mm-40) REVERT: B 1089 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: C 487 PHE cc_start: 0.7202 (t80) cc_final: 0.6985 (t80) REVERT: C 672 GLN cc_start: 0.7773 (mt0) cc_final: 0.7555 (mt0) REVERT: L 24 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7522 (tpp-160) REVERT: L 80 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6594 (mp0) REVERT: H 82 GLU cc_start: 0.7786 (tt0) cc_final: 0.7585 (tt0) REVERT: H 180 LEU cc_start: 0.8872 (mm) cc_final: 0.8584 (mt) REVERT: F 107 GLU cc_start: 0.7383 (pt0) cc_final: 0.6899 (tt0) REVERT: E 81 MET cc_start: 0.8582 (ttp) cc_final: 0.8354 (ttp) REVERT: E 183 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (mp) REVERT: K 27 GLN cc_start: 0.8094 (mp10) cc_final: 0.7709 (mp10) REVERT: K 55 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7900 (mtm-85) REVERT: J 6 GLN cc_start: 0.8261 (mt0) cc_final: 0.7945 (mt0) REVERT: J 180 LEU cc_start: 0.8555 (mt) cc_final: 0.8309 (tt) outliers start: 87 outliers final: 48 residues processed: 397 average time/residue: 1.5163 time to fit residues: 719.1433 Evaluate side-chains 382 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 323 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 307 optimal weight: 0.0370 chunk 170 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 285 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 370 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B 81 ASN B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B1103 GLN B1116 ASN C 748 ASN C 954 GLN C 999 GLN H 59 ASN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35101 Z= 0.327 Angle : 0.565 11.831 47770 Z= 0.290 Chirality : 0.046 0.380 5665 Planarity : 0.004 0.048 6049 Dihedral : 6.518 64.809 6151 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 11.07 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.51 (0.13), residues: 4267 helix: 1.43 (0.20), residues: 734 sheet: 0.61 (0.14), residues: 1312 loop : -0.13 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 108 HIS 0.004 0.001 HIS C1061 PHE 0.020 0.002 PHE B 168 TYR 0.025 0.002 TYR C 366 ARG 0.010 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 333 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 63 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7142 (p) REVERT: A 311 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: A 445 ASN cc_start: 0.8604 (t0) cc_final: 0.7994 (t160) REVERT: A 447 ASN cc_start: 0.8509 (m110) cc_final: 0.8164 (m110) REVERT: A 449 LEU cc_start: 0.8368 (mt) cc_final: 0.8067 (mt) REVERT: A 752 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: A 787 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7508 (mmpt) REVERT: A 805 ASP cc_start: 0.7346 (m-30) cc_final: 0.6698 (m-30) REVERT: A 954 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7414 (tp40) REVERT: A 1007 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: B 129 LYS cc_start: 0.7691 (mttt) cc_final: 0.7230 (mmpt) REVERT: B 375 LYS cc_start: 0.8262 (mttt) cc_final: 0.7564 (mtmt) REVERT: B 526 LYS cc_start: 0.8817 (mttt) cc_final: 0.8462 (mmtt) REVERT: B 574 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7288 (ttm110) REVERT: B 658 GLU cc_start: 0.7788 (tt0) cc_final: 0.7513 (tt0) REVERT: B 1089 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: C 405 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7368 (ptm-80) REVERT: C 455 LYS cc_start: 0.7977 (tppt) cc_final: 0.7662 (tppt) REVERT: C 672 GLN cc_start: 0.7776 (mt0) cc_final: 0.7555 (mt0) REVERT: L 24 ARG cc_start: 0.7779 (tpp-160) cc_final: 0.7497 (ttm110) REVERT: L 80 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6574 (mp0) REVERT: H 82 GLU cc_start: 0.7834 (tt0) cc_final: 0.7623 (tt0) REVERT: F 107 GLU cc_start: 0.7406 (pt0) cc_final: 0.6957 (tt0) REVERT: E 81 MET cc_start: 0.8606 (ttp) cc_final: 0.8346 (ttp) REVERT: E 183 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7575 (mp) REVERT: K 27 GLN cc_start: 0.8125 (mp10) cc_final: 0.7707 (mp10) REVERT: K 55 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7951 (mtm-85) REVERT: J 67 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7261 (mtm110) REVERT: J 180 LEU cc_start: 0.8555 (mt) cc_final: 0.8284 (tt) outliers start: 114 outliers final: 66 residues processed: 404 average time/residue: 1.4731 time to fit residues: 712.2028 Evaluate side-chains 390 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 312 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 74 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 9.9990 chunk 371 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 242 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 342 optimal weight: 40.0000 chunk 191 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN B 81 ASN B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN C 81 ASN C 801 GLN C 954 GLN C 999 GLN L 162 GLN H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35101 Z= 0.224 Angle : 0.530 10.803 47770 Z= 0.271 Chirality : 0.045 0.378 5665 Planarity : 0.004 0.057 6049 Dihedral : 6.149 59.958 6151 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.67 % Allowed : 11.66 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.56 (0.13), residues: 4267 helix: 1.50 (0.20), residues: 741 sheet: 0.63 (0.14), residues: 1313 loop : -0.11 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 108 HIS 0.005 0.001 HIS B 207 PHE 0.019 0.001 PHE B 397 TYR 0.026 0.001 TYR C 366 ARG 0.013 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 332 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: A 63 THR cc_start: 0.7762 (OUTLIER) cc_final: 0.7177 (p) REVERT: A 266 TYR cc_start: 0.7474 (m-80) cc_final: 0.7243 (m-80) REVERT: A 268 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: A 311 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: A 445 ASN cc_start: 0.8612 (t0) cc_final: 0.8000 (t160) REVERT: A 447 ASN cc_start: 0.8506 (m110) cc_final: 0.8167 (m110) REVERT: A 449 LEU cc_start: 0.8353 (mt) cc_final: 0.8045 (mt) REVERT: A 752 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: A 787 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7489 (mmpt) REVERT: A 805 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: A 926 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8175 (m) REVERT: A 954 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7406 (tp40) REVERT: A 1007 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: B 129 LYS cc_start: 0.7650 (mttt) cc_final: 0.7211 (mmpt) REVERT: B 237 ARG cc_start: 0.7570 (mtp85) cc_final: 0.7341 (mtm110) REVERT: B 375 LYS cc_start: 0.8262 (mttt) cc_final: 0.7601 (mtmt) REVERT: B 526 LYS cc_start: 0.8825 (mttt) cc_final: 0.8475 (mmtt) REVERT: B 574 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7263 (ttm110) REVERT: B 658 GLU cc_start: 0.7759 (tt0) cc_final: 0.7455 (tt0) REVERT: B 1089 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: C 672 GLN cc_start: 0.7758 (mt0) cc_final: 0.7547 (mt0) REVERT: L 24 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7492 (ttm110) REVERT: L 80 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6541 (mp0) REVERT: L 82 GLU cc_start: 0.8534 (pm20) cc_final: 0.8281 (pm20) REVERT: H 180 LEU cc_start: 0.8870 (mm) cc_final: 0.8551 (tp) REVERT: H 183 LEU cc_start: 0.8083 (pp) cc_final: 0.7809 (pt) REVERT: F 107 GLU cc_start: 0.7377 (pt0) cc_final: 0.6949 (tt0) REVERT: E 81 MET cc_start: 0.8580 (ttp) cc_final: 0.8307 (ttp) REVERT: E 183 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7483 (mp) REVERT: K 27 GLN cc_start: 0.8112 (mp10) cc_final: 0.7700 (mp10) REVERT: K 55 ARG cc_start: 0.8242 (mtm110) cc_final: 0.7956 (mtm-85) REVERT: K 107 GLU cc_start: 0.7202 (pt0) cc_final: 0.6989 (pt0) REVERT: J 67 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7220 (mtm110) REVERT: J 180 LEU cc_start: 0.8542 (mt) cc_final: 0.8284 (tt) outliers start: 100 outliers final: 54 residues processed: 394 average time/residue: 1.5633 time to fit residues: 738.2534 Evaluate side-chains 387 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 74 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 347 optimal weight: 7.9990 chunk 230 optimal weight: 0.4980 chunk 411 optimal weight: 0.0370 chunk 257 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN A1116 ASN B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 999 GLN C1122 ASN H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35101 Z= 0.244 Angle : 0.537 10.739 47770 Z= 0.274 Chirality : 0.045 0.377 5665 Planarity : 0.004 0.054 6049 Dihedral : 5.972 57.761 6151 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.59 % Allowed : 12.01 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.56 (0.13), residues: 4267 helix: 1.49 (0.19), residues: 741 sheet: 0.64 (0.14), residues: 1313 loop : -0.11 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 108 HIS 0.003 0.001 HIS C1061 PHE 0.020 0.001 PHE B 168 TYR 0.027 0.001 TYR C 366 ARG 0.011 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 319 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 63 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7183 (p) REVERT: A 268 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7700 (mt0) REVERT: A 311 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 445 ASN cc_start: 0.8613 (t0) cc_final: 0.8004 (t160) REVERT: A 447 ASN cc_start: 0.8501 (m110) cc_final: 0.8157 (m110) REVERT: A 449 LEU cc_start: 0.8358 (mt) cc_final: 0.8049 (mt) REVERT: A 752 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: A 787 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7505 (mmpt) REVERT: A 805 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: A 926 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.8181 (m) REVERT: A 954 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7408 (tp40) REVERT: A 1007 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: B 129 LYS cc_start: 0.7667 (mttt) cc_final: 0.7222 (mmpt) REVERT: B 237 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7310 (mtm110) REVERT: B 375 LYS cc_start: 0.8260 (mttt) cc_final: 0.7599 (mtmt) REVERT: B 526 LYS cc_start: 0.8830 (mttt) cc_final: 0.8474 (mmtt) REVERT: B 574 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7295 (ttm110) REVERT: B 658 GLU cc_start: 0.7777 (tt0) cc_final: 0.7475 (tt0) REVERT: B 1089 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: C 405 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7347 (ptm-80) REVERT: C 897 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8698 (mtp) REVERT: L 24 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7460 (ttm110) REVERT: L 80 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6503 (mp0) REVERT: L 185 LYS cc_start: 0.6182 (mmmt) cc_final: 0.5413 (tppt) REVERT: L 189 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7435 (mm-30) REVERT: H 180 LEU cc_start: 0.8857 (mm) cc_final: 0.8508 (tp) REVERT: H 183 LEU cc_start: 0.8054 (pp) cc_final: 0.7789 (pt) REVERT: F 107 GLU cc_start: 0.7373 (pt0) cc_final: 0.6982 (tt0) REVERT: E 183 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7459 (mp) REVERT: K 27 GLN cc_start: 0.8125 (mp10) cc_final: 0.7697 (mp10) REVERT: K 55 ARG cc_start: 0.8249 (mtm110) cc_final: 0.7953 (mtm-85) REVERT: J 38 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.6993 (ttt180) REVERT: J 67 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7224 (mtm110) REVERT: J 180 LEU cc_start: 0.8541 (mt) cc_final: 0.8267 (tt) outliers start: 97 outliers final: 58 residues processed: 378 average time/residue: 1.5460 time to fit residues: 697.1108 Evaluate side-chains 386 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 311 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 574 ARG Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 203 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN A 610 GLN A 759 GLN B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35101 Z= 0.185 Angle : 0.524 10.597 47770 Z= 0.265 Chirality : 0.044 0.405 5665 Planarity : 0.004 0.072 6049 Dihedral : 5.646 59.530 6150 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.30 % Allowed : 12.52 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.66 (0.13), residues: 4267 helix: 1.70 (0.20), residues: 735 sheet: 0.65 (0.14), residues: 1327 loop : -0.05 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.003 0.001 HIS B 207 PHE 0.023 0.001 PHE C 589 TYR 0.027 0.001 TYR C 366 ARG 0.019 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 340 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: A 63 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7220 (p) REVERT: A 266 TYR cc_start: 0.7600 (m-80) cc_final: 0.7356 (m-80) REVERT: A 268 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7629 (mt0) REVERT: A 311 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: A 445 ASN cc_start: 0.8621 (t0) cc_final: 0.8009 (t160) REVERT: A 447 ASN cc_start: 0.8490 (m110) cc_final: 0.8157 (m110) REVERT: A 449 LEU cc_start: 0.8367 (mt) cc_final: 0.8054 (mt) REVERT: A 752 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: A 787 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7603 (mmpt) REVERT: A 805 ASP cc_start: 0.7219 (m-30) cc_final: 0.6568 (m-30) REVERT: A 926 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8163 (m) REVERT: A 954 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7403 (tp40) REVERT: A 1007 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 129 LYS cc_start: 0.7757 (mttt) cc_final: 0.7302 (mmpt) REVERT: B 237 ARG cc_start: 0.7437 (mtp85) cc_final: 0.7220 (mtm110) REVERT: B 375 LYS cc_start: 0.8258 (mttt) cc_final: 0.7600 (mtmt) REVERT: B 526 LYS cc_start: 0.8813 (mttt) cc_final: 0.8478 (mmtt) REVERT: B 658 GLU cc_start: 0.7757 (tt0) cc_final: 0.7481 (tt0) REVERT: B 932 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: B 1089 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: C 737 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7749 (ttt) REVERT: L 24 ARG cc_start: 0.7814 (tpp-160) cc_final: 0.7475 (ttm110) REVERT: L 80 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6534 (mp0) REVERT: H 180 LEU cc_start: 0.8838 (mm) cc_final: 0.8530 (tp) REVERT: H 183 LEU cc_start: 0.8010 (pp) cc_final: 0.7788 (pt) REVERT: F 107 GLU cc_start: 0.7330 (pt0) cc_final: 0.6980 (tt0) REVERT: E 183 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7454 (mp) REVERT: K 27 GLN cc_start: 0.8123 (mp10) cc_final: 0.7680 (mp10) REVERT: K 55 ARG cc_start: 0.8244 (mtm110) cc_final: 0.7946 (mtm-85) REVERT: J 38 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7066 (ttt180) REVERT: J 180 LEU cc_start: 0.8542 (mt) cc_final: 0.8300 (tt) outliers start: 86 outliers final: 51 residues processed: 389 average time/residue: 1.4921 time to fit residues: 694.9154 Evaluate side-chains 385 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 932 GLN Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 38 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 8.9990 chunk 394 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 230 optimal weight: 0.3980 chunk 167 optimal weight: 0.3980 chunk 301 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 362 optimal weight: 50.0000 chunk 382 optimal weight: 50.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN B1116 ASN C 801 GLN C 999 GLN H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 GLN K 162 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 35101 Z= 0.473 Angle : 0.638 12.290 47770 Z= 0.327 Chirality : 0.050 0.551 5665 Planarity : 0.005 0.066 6049 Dihedral : 5.916 59.120 6149 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.67 % Allowed : 12.25 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 4267 helix: 1.09 (0.19), residues: 741 sheet: 0.57 (0.14), residues: 1309 loop : -0.23 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 108 HIS 0.006 0.001 HIS C1045 PHE 0.029 0.002 PHE B 397 TYR 0.024 0.002 TYR C1064 ARG 0.013 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 327 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: A 63 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7194 (p) REVERT: A 118 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8114 (tp) REVERT: A 190 ARG cc_start: 0.6506 (mtt-85) cc_final: 0.6284 (mtt90) REVERT: A 311 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: A 445 ASN cc_start: 0.8597 (t0) cc_final: 0.7975 (t160) REVERT: A 447 ASN cc_start: 0.8513 (m110) cc_final: 0.8143 (m110) REVERT: A 449 LEU cc_start: 0.8412 (mt) cc_final: 0.8094 (mt) REVERT: A 752 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: A 787 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7581 (mmpt) REVERT: A 805 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: A 954 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7310 (tp-100) REVERT: A 1007 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: B 129 LYS cc_start: 0.7762 (mttt) cc_final: 0.7295 (mmpt) REVERT: B 237 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7227 (mtm110) REVERT: B 266 TYR cc_start: 0.7789 (m-80) cc_final: 0.7520 (m-80) REVERT: B 375 LYS cc_start: 0.8261 (mttt) cc_final: 0.7573 (mtmt) REVERT: B 526 LYS cc_start: 0.8817 (mttt) cc_final: 0.8428 (mmtt) REVERT: B 658 GLU cc_start: 0.7823 (tt0) cc_final: 0.7543 (tt0) REVERT: B 1089 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: L 14 SER cc_start: 0.8277 (m) cc_final: 0.7957 (p) REVERT: L 24 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7582 (ttm110) REVERT: L 80 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6456 (mp0) REVERT: H 180 LEU cc_start: 0.8860 (mm) cc_final: 0.8528 (tp) REVERT: H 183 LEU cc_start: 0.8080 (pp) cc_final: 0.7852 (pt) REVERT: F 107 GLU cc_start: 0.7379 (pt0) cc_final: 0.7037 (tt0) REVERT: E 183 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7474 (mp) REVERT: K 27 GLN cc_start: 0.8149 (mp10) cc_final: 0.7709 (mp10) REVERT: K 55 ARG cc_start: 0.8283 (mtm110) cc_final: 0.7990 (mtm-85) REVERT: K 94 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8351 (p) REVERT: J 38 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7025 (ttt180) REVERT: J 67 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7346 (mtm110) REVERT: J 81 MET cc_start: 0.8451 (tmm) cc_final: 0.7671 (tmm) REVERT: J 180 LEU cc_start: 0.8538 (mt) cc_final: 0.8294 (tt) outliers start: 100 outliers final: 67 residues processed: 394 average time/residue: 1.5360 time to fit residues: 725.8708 Evaluate side-chains 393 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 312 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 5.9990 chunk 405 optimal weight: 30.0000 chunk 247 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 281 optimal weight: 0.6980 chunk 425 optimal weight: 40.0000 chunk 391 optimal weight: 4.9990 chunk 338 optimal weight: 50.0000 chunk 35 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 207 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN C 801 GLN C 999 GLN H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35101 Z= 0.291 Angle : 0.580 11.115 47770 Z= 0.296 Chirality : 0.046 0.556 5665 Planarity : 0.004 0.087 6049 Dihedral : 5.713 58.613 6149 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.35 % Allowed : 12.78 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % 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: 0.40 (0.13), residues: 4267 helix: 1.28 (0.19), residues: 742 sheet: 0.61 (0.14), residues: 1288 loop : -0.22 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 108 HIS 0.003 0.001 HIS A1045 PHE 0.026 0.001 PHE B 397 TYR 0.026 0.001 TYR C 366 ARG 0.022 0.001 ARG K 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 323 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 63 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 190 ARG cc_start: 0.6595 (mtt-85) cc_final: 0.6385 (mtt90) REVERT: A 268 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7704 (mt0) REVERT: A 311 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: A 445 ASN cc_start: 0.8591 (t0) cc_final: 0.7980 (t160) REVERT: A 447 ASN cc_start: 0.8509 (m110) cc_final: 0.8142 (m110) REVERT: A 449 LEU cc_start: 0.8390 (mt) cc_final: 0.8069 (mt) REVERT: A 752 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: A 787 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7548 (mmpt) REVERT: A 805 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: A 926 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8184 (m) REVERT: A 954 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: A 1007 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: B 129 LYS cc_start: 0.7687 (mttt) cc_final: 0.7225 (mmpt) REVERT: B 237 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7215 (mtm110) REVERT: B 375 LYS cc_start: 0.8254 (mttt) cc_final: 0.7580 (mtmt) REVERT: B 526 LYS cc_start: 0.8813 (mttt) cc_final: 0.8428 (mmtt) REVERT: B 658 GLU cc_start: 0.7793 (tt0) cc_final: 0.7532 (tt0) REVERT: B 1089 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: L 24 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7600 (ttm110) REVERT: L 185 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5785 (tppt) REVERT: H 180 LEU cc_start: 0.8855 (mm) cc_final: 0.8529 (tp) REVERT: H 183 LEU cc_start: 0.8040 (pp) cc_final: 0.7826 (pt) REVERT: F 107 GLU cc_start: 0.7348 (pt0) cc_final: 0.7018 (tt0) REVERT: E 183 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (mp) REVERT: K 27 GLN cc_start: 0.8147 (mp10) cc_final: 0.7720 (mp10) REVERT: K 55 ARG cc_start: 0.8265 (mtm110) cc_final: 0.7986 (mtm-85) REVERT: J 38 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7039 (ttt180) REVERT: J 67 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7298 (mtm110) REVERT: J 81 MET cc_start: 0.8446 (tmm) cc_final: 0.7658 (tmm) REVERT: J 180 LEU cc_start: 0.8530 (mt) cc_final: 0.8288 (tt) outliers start: 88 outliers final: 63 residues processed: 382 average time/residue: 1.4930 time to fit residues: 680.7467 Evaluate side-chains 388 residues out of total 3751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 311 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1114 THR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 67 ARG Chi-restraints excluded: chain J residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 269 optimal weight: 0.8980 chunk 360 optimal weight: 50.0000 chunk 103 optimal weight: 0.7980 chunk 312 optimal weight: 30.0000 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 339 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 391 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN C 801 GLN C 999 GLN H 3 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.202809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142099 restraints weight = 41139.542| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.83 r_work: 0.3280 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35101 Z= 0.211 Angle : 0.551 10.651 47770 Z= 0.279 Chirality : 0.045 0.703 5665 Planarity : 0.004 0.063 6049 Dihedral : 5.507 58.044 6149 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.06 % Allowed : 13.35 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.13), residues: 4267 helix: 1.51 (0.19), residues: 742 sheet: 0.64 (0.14), residues: 1303 loop : -0.16 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 108 HIS 0.003 0.001 HIS A1045 PHE 0.022 0.001 PHE C 589 TYR 0.028 0.001 TYR C 366 ARG 0.014 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13176.44 seconds wall clock time: 235 minutes 21.10 seconds (14121.10 seconds total)