Starting phenix.real_space_refine on Thu Feb 22 13:55:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9f_13868/02_2024/7q9f_13868.pdb" } resolution = 3.6 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= 0.003 sd= 0.020 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 148 5.16 5 C 21751 2.51 5 N 5609 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 339": "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: 34264 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7874 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 Chain: "B" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7848 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7926 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 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 Conformer: "B" Number of residues, atoms: 216, 1661 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 bond proxies already assigned to first conformer: 1689 Chain: "H" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 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 Conformer: "B" Number of residues, atoms: 216, 1661 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 bond proxies already assigned to first conformer: 1689 Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 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 Conformer: "B" Number of residues, atoms: 216, 1661 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 bond proxies already assigned to first conformer: 1689 Chain: "J" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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: 18.75, per 1000 atoms: 0.55 Number of scatterers: 34264 At special positions: 0 Unit cell: (160.72, 168.92, 215.66, 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 148 16.00 O 6756 8.00 N 5609 7.00 C 21751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.03 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=2.03 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 137 " - pdb=" SG ACYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG BCYS L 197 " 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 137 " - pdb=" SG ACYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG BCYS F 197 " 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 137 " - pdb=" SG ACYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG BCYS K 197 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 4 " " NAG V 1 " - " FUC V 4 " 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 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: 13.20 Conformation dependent library (CDL) restraints added in 6.9 seconds 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 85 sheets defined 20.3% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 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 362 through 368 removed outlier: 3.878A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.671A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.679A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.559A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.122A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 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 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 5.022A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.276A 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 368 removed outlier: 3.663A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.100A pdb=" N ASN B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.994A 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 499 through 502 Processing helix chain 'B' and resid 734 through 740 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 759 through 780 Processing helix chain 'B' and resid 798 through 802 removed outlier: 4.433A pdb=" N GLN B 801 " --> pdb=" O ASN B 798 " (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: 3.776A 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 915 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.862A pdb=" N ASN B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.031A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.442A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.983A 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 346 through 350 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.588A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.954A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.318A 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 734 through 740 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 759 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.837A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.696A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.166A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) 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: 3.912A 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 removed outlier: 3.650A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 5.121A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.717A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.509A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 124 through 130 removed outlier: 3.521A pdb=" N SER L 130 " --> pdb=" O GLU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 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 80 through 84 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.608A pdb=" N SER F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.555A pdb=" N GLN E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 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 80 through 84 removed outlier: 3.596A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 186 through 191 Processing helix chain 'J' and resid 87 through 91 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: 3.576A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 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 132 through 141 removed outlier: 6.458A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.570A pdb=" N TYR A 310 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.770A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (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: 6.937A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 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: 3.587A pdb=" N ALA A 691 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.574A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 725 removed outlier: 3.555A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.064A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.378A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.729A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.534A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.521A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 132 through 141 removed outlier: 6.129A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 314 removed outlier: 3.714A pdb=" N TYR B 310 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.802A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.705A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.743A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.925A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 Processing sheet with id=AD7, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'B' and resid 1083 through 1087 removed outlier: 4.282A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.733A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.176A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 135 through 142 removed outlier: 6.804A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 275 through 276 removed outlier: 7.083A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N TYR C 310 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.229A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.536A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.828A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.237A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.250A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'L' and resid 117 through 121 removed outlier: 5.290A pdb=" N SER L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU L 184 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 182 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 138 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER L 180 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN L 140 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU L 178 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 156 through 158 removed outlier: 4.531A pdb=" N TRP L 151 " --> pdb=" O GLN L 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N VAL H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG9, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.122A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 117 through 121 removed outlier: 5.549A pdb=" N TYR F 176 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 157 through 158 removed outlier: 4.689A pdb=" N TRP F 151 " --> pdb=" O GLN F 158 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AH8, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.827A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 155 through 159 removed outlier: 4.336A pdb=" N TYR E 199 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.322A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AI7, first strand: chain 'K' and resid 117 through 121 removed outlier: 5.307A pdb=" N SER K 134 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU K 184 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL K 136 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 182 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU K 138 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER K 180 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN K 140 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU K 178 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 156 through 158 removed outlier: 4.521A pdb=" N TRP K 151 " --> pdb=" O GLN K 158 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AJ1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.778A pdb=" N PHE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.377A pdb=" N TYR J 199 " --> pdb=" O VAL J 216 " (cutoff:3.500A) 1478 hydrogen bonds defined for protein. 3846 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: 17.70 Time building geometry restraints manager: 14.27 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: 10853 1.34 - 1.46: 8539 1.46 - 1.58: 15460 1.58 - 1.70: 0 1.70 - 1.82: 188 Bond restraints: 35040 Sorted by residual: bond pdb=" N ASP K 1 " pdb=" CA ASP K 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 35035 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.64: 1071 106.64 - 113.48: 19477 113.48 - 120.32: 12098 120.32 - 127.16: 14707 127.16 - 134.00: 346 Bond angle restraints: 47699 Sorted by residual: angle pdb=" N THR C 615 " pdb=" CA THR C 615 " pdb=" C THR C 615 " ideal model delta sigma weight residual 114.62 110.79 3.83 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.62 111.17 3.45 1.14e+00 7.69e-01 9.18e+00 angle pdb=" CA THR C 615 " pdb=" C THR C 615 " pdb=" N GLU C 616 " ideal model delta sigma weight residual 119.71 116.84 2.87 1.17e+00 7.31e-01 6.03e+00 angle pdb=" C GLY K 51 " pdb=" N ALA K 52 " pdb=" CA ALA K 52 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.58e+00 angle pdb=" C3 BMA P 3 " pdb=" C2 BMA P 3 " pdb=" O2 BMA P 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.45e+00 ... (remaining 47694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 21052 22.05 - 44.10: 554 44.10 - 66.15: 79 66.15 - 88.20: 31 88.20 - 110.24: 9 Dihedral angle restraints: 21725 sinusoidal: 9196 harmonic: 12529 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 -125.08 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" O4 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C5 BMA V 3 " pdb=" O5 BMA V 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.47 110.24 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.66 109.05 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 21722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4763 0.055 - 0.111: 689 0.111 - 0.166: 153 0.166 - 0.222: 3 0.222 - 0.277: 2 Chirality restraints: 5610 Sorted by residual: 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 0.28 2.00e-01 2.50e+01 1.92e+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 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 5607 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO E 154 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 153 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO J 154 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " -0.020 5.00e-02 4.00e+02 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 305 2.53 - 3.12: 27264 3.12 - 3.72: 51836 3.72 - 4.31: 75264 4.31 - 4.90: 126249 Nonbonded interactions: 280918 Sorted by model distance: nonbonded pdb=" OG1 THR A 390 " pdb=" O GLU A 513 " model vdw 1.941 2.440 nonbonded pdb=" OG1 THR B 390 " pdb=" O GLU B 513 " model vdw 2.012 2.440 nonbonded pdb=" OG SER B 356 " pdb=" OD1 ASN B 391 " model vdw 2.037 2.440 nonbonded pdb=" O TYR F 189 " pdb=" OH TYR F 195 " model vdw 2.060 2.440 nonbonded pdb=" OD1 ASP B 361 " pdb=" N TYR B 362 " model vdw 2.110 2.520 ... (remaining 280913 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 25 through 242 or (resid 243 and (name N or name CA or nam \ e C or name O or name CB )) or resid 262 through 617 or resid 638 through 1144 o \ r resid 1301 through 1308)) selection = (chain 'B' and (resid 25 through 1144 or resid 1301 through 1308)) selection = (chain 'C' and (resid 25 through 143 or resid 156 through 617 or resid 638 throu \ gh 1144 or resid 1301 through 1308)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'F' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'K' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'L' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) } 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' } ncs_group { reference = chain 'P' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.110 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: 16.560 Check model and map are aligned: 0.510 Set scattering table: 0.330 Process input model: 94.910 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 35040 Z= 0.230 Angle : 0.509 6.332 47699 Z= 0.253 Chirality : 0.044 0.277 5610 Planarity : 0.003 0.047 6065 Dihedral : 10.299 110.244 13517 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.45 % Allowed : 3.77 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4252 helix: 0.93 (0.20), residues: 730 sheet: 0.37 (0.15), residues: 1276 loop : -0.27 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 102 HIS 0.003 0.001 HIS A 652 PHE 0.009 0.001 PHE B 92 TYR 0.015 0.001 TYR B1064 ARG 0.002 0.000 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 387 time to evaluate : 4.043 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: 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 486 TYR cc_start: 0.8782 (m-80) cc_final: 0.8335 (m-80) REVERT: B 220 PHE cc_start: 0.7251 (t80) cc_final: 0.6613 (t80) REVERT: B 520 THR cc_start: 0.7611 (p) cc_final: 0.7327 (p) REVERT: B 899 MET cc_start: 0.9067 (mmm) cc_final: 0.8650 (tpt) REVERT: C 267 LEU cc_start: 0.8583 (mt) cc_final: 0.7948 (mt) REVERT: C 350 TRP cc_start: 0.8205 (p-90) cc_final: 0.7677 (p-90) REVERT: C 399 ILE cc_start: 0.8367 (pt) cc_final: 0.8083 (pt) REVERT: C 449 LEU cc_start: 0.9260 (mt) cc_final: 0.9053 (mm) REVERT: C 502 TYR cc_start: 0.9028 (m-80) cc_final: 0.8717 (m-10) REVERT: C 866 MET cc_start: 0.8831 (mtt) cc_final: 0.8515 (ttm) REVERT: C 899 MET cc_start: 0.8942 (mmm) cc_final: 0.8633 (tpt) REVERT: L 33 TYR cc_start: 0.8672 (m-80) cc_final: 0.8030 (m-80) REVERT: L 91 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (pp30) REVERT: H 32 TYR cc_start: 0.8840 (m-10) cc_final: 0.8580 (m-80) REVERT: H 48 MET cc_start: 0.8615 (mtp) cc_final: 0.8297 (mtp) REVERT: H 82 GLU cc_start: 0.9207 (tt0) cc_final: 0.8988 (tp30) REVERT: H 107 MET cc_start: 0.9106 (mmm) cc_final: 0.8888 (mmm) REVERT: F 4 MET cc_start: 0.7907 (mmm) cc_final: 0.7293 (mmm) REVERT: F 36 TRP cc_start: 0.8321 (m100) cc_final: 0.7944 (m100) REVERT: E 46 GLU cc_start: 0.8533 (tt0) cc_final: 0.8043 (pt0) REVERT: E 48 MET cc_start: 0.8650 (mtp) cc_final: 0.8269 (mtp) REVERT: E 197 GLN cc_start: 0.8337 (tp40) cc_final: 0.7743 (tm-30) REVERT: E 211 LYS cc_start: 0.9169 (mttm) cc_final: 0.8915 (tptp) REVERT: K 61 ASP cc_start: 0.9140 (p0) cc_final: 0.8811 (p0) outliers start: 17 outliers final: 7 residues processed: 404 average time/residue: 0.6017 time to fit residues: 361.6372 Evaluate side-chains 209 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 218 optimal weight: 20.0000 chunk 172 optimal weight: 0.0060 chunk 334 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 387 optimal weight: 40.0000 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 196 ASN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN H 176 GLN F 38 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 204 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35040 Z= 0.215 Angle : 0.547 9.726 47699 Z= 0.280 Chirality : 0.044 0.207 5610 Planarity : 0.004 0.050 6065 Dihedral : 7.186 69.792 5971 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.55 % Allowed : 7.50 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.41 (0.13), residues: 4252 helix: 1.60 (0.20), residues: 749 sheet: 0.47 (0.14), residues: 1302 loop : -0.25 (0.14), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 108 HIS 0.007 0.001 HIS F 192 PHE 0.037 0.002 PHE C 135 TYR 0.022 0.001 TYR L 99 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 4.033 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: 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 118 LEU cc_start: 0.9605 (tp) cc_final: 0.9254 (mp) REVERT: A 486 TYR cc_start: 0.8888 (m-80) cc_final: 0.8269 (m-10) REVERT: B 133 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: B 210 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8000 (tp) REVERT: B 520 THR cc_start: 0.7670 (p) cc_final: 0.7382 (p) REVERT: B 899 MET cc_start: 0.9018 (mmm) cc_final: 0.8524 (tpt) REVERT: C 229 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8087 (tp) REVERT: C 350 TRP cc_start: 0.8338 (p-90) cc_final: 0.7768 (p-90) REVERT: C 399 ILE cc_start: 0.8297 (pt) cc_final: 0.8020 (pt) REVERT: C 502 TYR cc_start: 0.9025 (m-80) cc_final: 0.8778 (m-10) REVERT: C 737 MET cc_start: 0.7830 (tpp) cc_final: 0.7581 (tpt) REVERT: C 866 MET cc_start: 0.8832 (mtt) cc_final: 0.8536 (ttm) REVERT: H 10 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6375 (mm-30) REVERT: H 48 MET cc_start: 0.8569 (mtp) cc_final: 0.8324 (mtp) REVERT: H 80 TYR cc_start: 0.8836 (m-80) cc_final: 0.8456 (m-10) REVERT: H 81 MET cc_start: 0.8009 (ppp) cc_final: 0.7517 (ppp) REVERT: H 82 GLU cc_start: 0.9065 (tt0) cc_final: 0.8795 (tp30) REVERT: F 4 MET cc_start: 0.8071 (mmm) cc_final: 0.7133 (mmm) REVERT: F 36 TRP cc_start: 0.8109 (m100) cc_final: 0.7858 (m100) REVERT: E 48 MET cc_start: 0.8698 (mtp) cc_final: 0.7935 (mtp) REVERT: E 67 ARG cc_start: 0.8294 (mtp180) cc_final: 0.8055 (ttp-170) REVERT: E 211 LYS cc_start: 0.9152 (mttm) cc_final: 0.8921 (tptp) REVERT: K 2 ILE cc_start: 0.8926 (mm) cc_final: 0.8607 (tp) REVERT: K 61 ASP cc_start: 0.9171 (p0) cc_final: 0.8858 (p0) REVERT: J 10 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7480 (mm-30) REVERT: J 107 MET cc_start: 0.8253 (mtt) cc_final: 0.7987 (mtt) outliers start: 58 outliers final: 35 residues processed: 291 average time/residue: 0.6165 time to fit residues: 271.0070 Evaluate side-chains 220 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 152 LYS Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 419 optimal weight: 50.0000 chunk 345 optimal weight: 0.5980 chunk 385 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 GLN B 771 GLN ** B 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 904 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 35040 Z= 0.382 Angle : 0.589 9.247 47699 Z= 0.299 Chirality : 0.045 0.285 5610 Planarity : 0.004 0.060 6065 Dihedral : 6.397 59.791 5968 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.82 % Allowed : 8.92 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.18 (0.13), residues: 4252 helix: 1.38 (0.19), residues: 751 sheet: 0.38 (0.14), residues: 1307 loop : -0.43 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1099 HIS 0.008 0.001 HIS A 652 PHE 0.038 0.002 PHE C 135 TYR 0.034 0.001 TYR L 99 ARG 0.010 0.001 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 3.859 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: A 118 LEU cc_start: 0.9629 (tp) cc_final: 0.9357 (mp) REVERT: A 486 TYR cc_start: 0.8864 (m-80) cc_final: 0.8302 (m-80) REVERT: B 133 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: B 210 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7898 (tp) REVERT: B 520 THR cc_start: 0.7810 (p) cc_final: 0.7548 (p) REVERT: B 899 MET cc_start: 0.9024 (mmm) cc_final: 0.8498 (tpt) REVERT: C 51 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (p) REVERT: C 229 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8072 (tp) REVERT: C 350 TRP cc_start: 0.8496 (p-90) cc_final: 0.7823 (p-90) REVERT: C 399 ILE cc_start: 0.8334 (pt) cc_final: 0.8052 (pt) REVERT: C 502 TYR cc_start: 0.9047 (m-80) cc_final: 0.8805 (m-10) REVERT: C 737 MET cc_start: 0.7887 (tpp) cc_final: 0.7629 (tpt) REVERT: C 866 MET cc_start: 0.8910 (mtt) cc_final: 0.8578 (ttm) REVERT: H 10 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6513 (mm-30) REVERT: H 32 TYR cc_start: 0.8800 (m-80) cc_final: 0.8261 (m-80) REVERT: H 80 TYR cc_start: 0.8878 (m-80) cc_final: 0.8390 (m-10) REVERT: F 4 MET cc_start: 0.8167 (mmm) cc_final: 0.7693 (mmm) REVERT: F 36 TRP cc_start: 0.8219 (m100) cc_final: 0.7883 (m100) REVERT: F 97 ARG cc_start: 0.8730 (mtp-110) cc_final: 0.8421 (mtp85) REVERT: E 29 PHE cc_start: 0.7826 (t80) cc_final: 0.7617 (t80) REVERT: E 48 MET cc_start: 0.8682 (mtp) cc_final: 0.8221 (mtp) REVERT: E 67 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7997 (ttp-170) REVERT: E 197 GLN cc_start: 0.8346 (tp40) cc_final: 0.7773 (tm-30) REVERT: K 2 ILE cc_start: 0.8922 (mm) cc_final: 0.8679 (tp) REVERT: K 61 ASP cc_start: 0.9173 (p0) cc_final: 0.8842 (p0) REVERT: K 97 ARG cc_start: 0.8312 (mmt180) cc_final: 0.8096 (mmt180) REVERT: J 10 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7461 (mm-30) REVERT: J 48 MET cc_start: 0.8509 (mtt) cc_final: 0.8114 (tpp) REVERT: J 107 MET cc_start: 0.8298 (mtt) cc_final: 0.8049 (mtt) outliers start: 68 outliers final: 42 residues processed: 269 average time/residue: 0.5635 time to fit residues: 234.3300 Evaluate side-chains 232 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 50.0000 chunk 292 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 260 optimal weight: 0.9990 chunk 389 optimal weight: 30.0000 chunk 412 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 369 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 GLN C 218 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN H 204 ASN F 38 GLN F 161 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 35040 Z= 0.298 Angle : 0.546 9.800 47699 Z= 0.278 Chirality : 0.044 0.280 5610 Planarity : 0.004 0.064 6065 Dihedral : 5.763 59.668 5968 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.87 % Allowed : 9.40 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 4252 helix: 1.38 (0.19), residues: 752 sheet: 0.38 (0.14), residues: 1286 loop : -0.49 (0.14), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 102 HIS 0.006 0.001 HIS F 201 PHE 0.033 0.002 PHE C 135 TYR 0.047 0.001 TYR L 99 ARG 0.008 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 197 time to evaluate : 3.895 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: A 92 PHE cc_start: 0.7868 (t80) cc_final: 0.7411 (t80) REVERT: A 118 LEU cc_start: 0.9624 (tp) cc_final: 0.9312 (mp) REVERT: A 461 PHE cc_start: 0.8366 (m-80) cc_final: 0.8063 (t80) REVERT: A 486 TYR cc_start: 0.8816 (m-80) cc_final: 0.8239 (m-80) REVERT: B 133 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: B 210 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7903 (tp) REVERT: B 520 THR cc_start: 0.7807 (p) cc_final: 0.7531 (p) REVERT: B 899 MET cc_start: 0.8997 (mmm) cc_final: 0.8387 (tpt) REVERT: B 1047 MET cc_start: 0.8465 (ptm) cc_final: 0.8248 (ptm) REVERT: C 350 TRP cc_start: 0.8505 (p-90) cc_final: 0.7844 (p-90) REVERT: C 399 ILE cc_start: 0.8355 (pt) cc_final: 0.8064 (pt) REVERT: C 502 TYR cc_start: 0.9041 (m-80) cc_final: 0.8815 (m-10) REVERT: C 737 MET cc_start: 0.7909 (tpp) cc_final: 0.7657 (tpt) REVERT: C 866 MET cc_start: 0.8888 (mtt) cc_final: 0.8544 (ttm) REVERT: L 80 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9048 (mm-30) REVERT: H 10 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6642 (mm-30) REVERT: H 32 TYR cc_start: 0.8769 (m-80) cc_final: 0.8295 (m-80) REVERT: H 48 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7950 (mtm) REVERT: H 65 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8079 (mm-40) REVERT: H 80 TYR cc_start: 0.8816 (m-80) cc_final: 0.8288 (m-10) REVERT: H 153 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8329 (mp0) REVERT: F 4 MET cc_start: 0.8213 (mmm) cc_final: 0.7854 (mmm) REVERT: F 36 TRP cc_start: 0.8219 (m100) cc_final: 0.7862 (m100) REVERT: F 97 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8426 (mtp85) REVERT: E 48 MET cc_start: 0.8626 (mtp) cc_final: 0.7669 (mtp) REVERT: E 67 ARG cc_start: 0.8172 (mtp180) cc_final: 0.6330 (ttp-170) REVERT: E 94 TYR cc_start: 0.8077 (m-80) cc_final: 0.7790 (m-80) REVERT: K 61 ASP cc_start: 0.9180 (p0) cc_final: 0.8845 (p0) REVERT: J 10 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7498 (mm-30) REVERT: J 48 MET cc_start: 0.8536 (mtt) cc_final: 0.8196 (tpp) REVERT: J 107 MET cc_start: 0.8289 (mtt) cc_final: 0.7929 (mtt) outliers start: 70 outliers final: 45 residues processed: 254 average time/residue: 0.5581 time to fit residues: 220.8504 Evaluate side-chains 227 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain K residue 152 LYS Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 20.0000 chunk 234 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 307 optimal weight: 40.0000 chunk 170 optimal weight: 0.8980 chunk 352 optimal weight: 1.9990 chunk 285 optimal weight: 0.0030 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 370 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN C1103 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN E 6 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 35040 Z= 0.159 Angle : 0.506 9.730 47699 Z= 0.257 Chirality : 0.043 0.221 5610 Planarity : 0.004 0.065 6065 Dihedral : 5.255 59.705 5968 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.36 % Allowed : 10.31 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.27 (0.13), residues: 4252 helix: 1.64 (0.20), residues: 755 sheet: 0.38 (0.15), residues: 1284 loop : -0.41 (0.14), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 102 HIS 0.004 0.001 HIS F 201 PHE 0.032 0.001 PHE C 453 TYR 0.046 0.001 TYR L 99 ARG 0.009 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 4.619 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: A 92 PHE cc_start: 0.7765 (t80) cc_final: 0.7338 (t80) REVERT: A 118 LEU cc_start: 0.9617 (tp) cc_final: 0.9304 (mp) REVERT: A 461 PHE cc_start: 0.8342 (m-80) cc_final: 0.7986 (t80) REVERT: A 486 TYR cc_start: 0.8830 (m-80) cc_final: 0.8239 (m-80) REVERT: A 914 TYR cc_start: 0.9154 (m-80) cc_final: 0.8769 (m-10) REVERT: B 133 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: B 210 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7861 (tp) REVERT: B 520 THR cc_start: 0.7680 (p) cc_final: 0.7429 (p) REVERT: B 899 MET cc_start: 0.8988 (mmm) cc_final: 0.8393 (tpt) REVERT: C 229 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7500 (tt) REVERT: C 350 TRP cc_start: 0.8426 (p-90) cc_final: 0.7827 (p-90) REVERT: C 399 ILE cc_start: 0.8312 (pt) cc_final: 0.8035 (pt) REVERT: C 502 TYR cc_start: 0.9023 (m-80) cc_final: 0.8805 (m-10) REVERT: L 80 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9053 (mm-30) REVERT: H 10 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6674 (mm-30) REVERT: H 32 TYR cc_start: 0.8723 (m-80) cc_final: 0.8261 (m-80) REVERT: H 48 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7911 (mtm) REVERT: H 80 TYR cc_start: 0.8752 (m-80) cc_final: 0.8443 (m-10) REVERT: H 153 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8258 (mp0) REVERT: F 4 MET cc_start: 0.8175 (mmm) cc_final: 0.7575 (mmm) REVERT: F 36 TRP cc_start: 0.8135 (m100) cc_final: 0.7732 (m100) REVERT: F 97 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8450 (mtp85) REVERT: E 48 MET cc_start: 0.8563 (mtp) cc_final: 0.7637 (mtp) REVERT: E 94 TYR cc_start: 0.8081 (m-80) cc_final: 0.7802 (m-80) REVERT: K 61 ASP cc_start: 0.9165 (p0) cc_final: 0.8826 (p0) REVERT: J 10 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7595 (mm-30) REVERT: J 107 MET cc_start: 0.8272 (mtt) cc_final: 0.7897 (mtt) outliers start: 51 outliers final: 39 residues processed: 246 average time/residue: 0.6074 time to fit residues: 234.3327 Evaluate side-chains 228 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 3.9990 chunk 371 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 413 optimal weight: 5.9990 chunk 342 optimal weight: 50.0000 chunk 191 optimal weight: 0.1980 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN F 161 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 35040 Z= 0.476 Angle : 0.618 8.936 47699 Z= 0.315 Chirality : 0.045 0.291 5610 Planarity : 0.004 0.050 6065 Dihedral : 5.390 58.653 5968 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.24 % Allowed : 10.49 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4252 helix: 1.17 (0.19), residues: 751 sheet: 0.29 (0.15), residues: 1284 loop : -0.61 (0.14), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 36 HIS 0.008 0.001 HIS A 652 PHE 0.035 0.002 PHE E 29 TYR 0.048 0.002 TYR L 99 ARG 0.009 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 195 time to evaluate : 3.974 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: A 92 PHE cc_start: 0.7872 (t80) cc_final: 0.7405 (t80) REVERT: A 118 LEU cc_start: 0.9633 (tp) cc_final: 0.9310 (mp) REVERT: A 486 TYR cc_start: 0.8817 (m-80) cc_final: 0.8241 (m-80) REVERT: A 1026 MET cc_start: 0.9336 (tpp) cc_final: 0.8562 (ttm) REVERT: B 133 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: B 210 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7839 (tp) REVERT: B 520 THR cc_start: 0.7867 (p) cc_final: 0.7575 (p) REVERT: B 899 MET cc_start: 0.9101 (mmm) cc_final: 0.8612 (tpt) REVERT: C 51 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 229 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7685 (tt) REVERT: C 350 TRP cc_start: 0.8562 (p-90) cc_final: 0.7870 (p-90) REVERT: C 399 ILE cc_start: 0.8427 (pt) cc_final: 0.8134 (pt) REVERT: C 502 TYR cc_start: 0.9055 (m-80) cc_final: 0.8798 (m-10) REVERT: C 866 MET cc_start: 0.8876 (mtm) cc_final: 0.8492 (ttm) REVERT: L 17 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8564 (mt-10) REVERT: L 80 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9022 (mm-30) REVERT: H 10 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6746 (mm-30) REVERT: H 32 TYR cc_start: 0.8770 (m-80) cc_final: 0.8216 (m-80) REVERT: H 80 TYR cc_start: 0.8780 (m-80) cc_final: 0.8242 (m-10) REVERT: F 4 MET cc_start: 0.8234 (mmm) cc_final: 0.8005 (mmm) REVERT: F 36 TRP cc_start: 0.8361 (m100) cc_final: 0.7796 (m100) REVERT: F 98 MET cc_start: 0.8472 (mpp) cc_final: 0.8109 (ptp) REVERT: E 48 MET cc_start: 0.8658 (mtp) cc_final: 0.7943 (mtp) REVERT: E 197 GLN cc_start: 0.8396 (tp40) cc_final: 0.7859 (tm-30) REVERT: K 61 ASP cc_start: 0.9178 (p0) cc_final: 0.8829 (p0) REVERT: J 10 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7576 (mm-30) REVERT: J 48 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8019 (mpp) REVERT: J 107 MET cc_start: 0.8327 (mtt) cc_final: 0.7953 (mtt) outliers start: 84 outliers final: 58 residues processed: 266 average time/residue: 0.5415 time to fit residues: 227.2052 Evaluate side-chains 244 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 181 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 301 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 347 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 250 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35040 Z= 0.194 Angle : 0.522 9.250 47699 Z= 0.264 Chirality : 0.043 0.239 5610 Planarity : 0.004 0.052 6065 Dihedral : 5.083 58.345 5968 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.63 % Allowed : 11.32 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.17 (0.13), residues: 4252 helix: 1.54 (0.20), residues: 753 sheet: 0.32 (0.14), residues: 1307 loop : -0.47 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 102 HIS 0.002 0.001 HIS A 652 PHE 0.030 0.001 PHE L 29 TYR 0.040 0.001 TYR L 99 ARG 0.007 0.000 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 3.838 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: A 92 PHE cc_start: 0.7810 (t80) cc_final: 0.7366 (t80) REVERT: A 118 LEU cc_start: 0.9626 (tp) cc_final: 0.9306 (mp) REVERT: A 461 PHE cc_start: 0.8315 (m-80) cc_final: 0.8004 (t80) REVERT: A 486 TYR cc_start: 0.8799 (m-80) cc_final: 0.8208 (m-80) REVERT: A 1026 MET cc_start: 0.9236 (tpp) cc_final: 0.8468 (ttm) REVERT: B 133 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: B 210 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7855 (tp) REVERT: B 520 THR cc_start: 0.7742 (p) cc_final: 0.7482 (p) REVERT: B 1138 LEU cc_start: 0.9126 (mp) cc_final: 0.8901 (pp) REVERT: C 229 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7540 (tt) REVERT: C 350 TRP cc_start: 0.8473 (p-90) cc_final: 0.7886 (p-90) REVERT: C 399 ILE cc_start: 0.8397 (pt) cc_final: 0.8117 (pt) REVERT: C 502 TYR cc_start: 0.9027 (m-80) cc_final: 0.8824 (m-10) REVERT: L 80 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9040 (mm-30) REVERT: H 10 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6788 (mm-30) REVERT: H 32 TYR cc_start: 0.8709 (m-80) cc_final: 0.8261 (m-80) REVERT: H 80 TYR cc_start: 0.8715 (m-80) cc_final: 0.8166 (m-10) REVERT: F 4 MET cc_start: 0.8134 (mmm) cc_final: 0.7711 (mmm) REVERT: F 36 TRP cc_start: 0.8203 (m100) cc_final: 0.7612 (m100) REVERT: F 98 MET cc_start: 0.8474 (mpp) cc_final: 0.8234 (ptp) REVERT: E 48 MET cc_start: 0.8540 (mtp) cc_final: 0.7689 (mtp) REVERT: E 94 TYR cc_start: 0.8111 (m-80) cc_final: 0.7869 (m-80) REVERT: K 61 ASP cc_start: 0.9162 (p0) cc_final: 0.8813 (p0) REVERT: K 97 ARG cc_start: 0.8423 (mmt180) cc_final: 0.8206 (mmt-90) REVERT: J 10 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7648 (mm-30) REVERT: J 48 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8143 (mpp) REVERT: J 107 MET cc_start: 0.8307 (mtt) cc_final: 0.7919 (mtt) outliers start: 61 outliers final: 49 residues processed: 245 average time/residue: 0.5375 time to fit residues: 205.9081 Evaluate side-chains 237 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1115 ASP Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 81 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 280 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 323 optimal weight: 30.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** J 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 35040 Z= 0.288 Angle : 0.546 12.200 47699 Z= 0.276 Chirality : 0.043 0.247 5610 Planarity : 0.004 0.053 6065 Dihedral : 5.061 57.345 5968 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.76 % Allowed : 11.56 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.12 (0.13), residues: 4252 helix: 1.49 (0.20), residues: 752 sheet: 0.32 (0.14), residues: 1298 loop : -0.53 (0.14), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.005 0.001 HIS A 652 PHE 0.051 0.001 PHE F 29 TYR 0.038 0.001 TYR F 99 ARG 0.011 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 4.049 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: A 92 PHE cc_start: 0.7817 (t80) cc_final: 0.7316 (t80) REVERT: A 118 LEU cc_start: 0.9631 (tp) cc_final: 0.9308 (mp) REVERT: A 461 PHE cc_start: 0.8323 (m-80) cc_final: 0.7978 (t80) REVERT: A 486 TYR cc_start: 0.8801 (m-80) cc_final: 0.8215 (m-80) REVERT: A 1026 MET cc_start: 0.9281 (tpp) cc_final: 0.8498 (ttm) REVERT: B 133 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: B 210 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7838 (tp) REVERT: B 520 THR cc_start: 0.7775 (p) cc_final: 0.7495 (p) REVERT: B 1138 LEU cc_start: 0.9139 (mp) cc_final: 0.8906 (pp) REVERT: C 58 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8707 (m-10) REVERT: C 229 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7526 (tt) REVERT: C 350 TRP cc_start: 0.8486 (p-90) cc_final: 0.7906 (p-90) REVERT: C 399 ILE cc_start: 0.8380 (pt) cc_final: 0.8088 (pt) REVERT: C 502 TYR cc_start: 0.9028 (m-80) cc_final: 0.8794 (m-10) REVERT: L 17 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8514 (mt-10) REVERT: L 80 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9046 (mm-30) REVERT: H 10 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6791 (mm-30) REVERT: H 32 TYR cc_start: 0.8720 (m-80) cc_final: 0.8231 (m-80) REVERT: H 80 TYR cc_start: 0.8718 (m-80) cc_final: 0.8169 (m-10) REVERT: F 4 MET cc_start: 0.8171 (mmm) cc_final: 0.7743 (mmm) REVERT: F 36 TRP cc_start: 0.8302 (m100) cc_final: 0.7696 (m100) REVERT: F 98 MET cc_start: 0.8425 (mpp) cc_final: 0.8210 (ptp) REVERT: E 23 LYS cc_start: 0.9209 (mttt) cc_final: 0.8989 (mppt) REVERT: E 48 MET cc_start: 0.8590 (mtp) cc_final: 0.8060 (mtp) REVERT: K 61 ASP cc_start: 0.9170 (p0) cc_final: 0.8823 (p0) REVERT: K 97 ARG cc_start: 0.8370 (mmt180) cc_final: 0.8065 (mmp-170) REVERT: J 10 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7646 (mm-30) REVERT: J 48 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8198 (mpp) REVERT: J 67 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: J 107 MET cc_start: 0.8325 (mtt) cc_final: 0.7929 (mtt) outliers start: 66 outliers final: 50 residues processed: 245 average time/residue: 0.5434 time to fit residues: 208.1313 Evaluate side-chains 234 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 179 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 884 THR Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 chunk 383 optimal weight: 50.0000 chunk 230 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 382 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** J 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 35040 Z= 0.441 Angle : 0.608 8.957 47699 Z= 0.309 Chirality : 0.045 0.262 5610 Planarity : 0.004 0.085 6065 Dihedral : 5.264 53.628 5968 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.79 % Allowed : 11.70 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: -0.10 (0.13), residues: 4252 helix: 1.20 (0.19), residues: 752 sheet: 0.21 (0.14), residues: 1317 loop : -0.65 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 104 HIS 0.006 0.001 HIS A 652 PHE 0.027 0.002 PHE F 29 TYR 0.035 0.002 TYR L 99 ARG 0.012 0.001 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 182 time to evaluate : 3.957 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: A 92 PHE cc_start: 0.7857 (t80) cc_final: 0.7384 (t80) REVERT: A 118 LEU cc_start: 0.9637 (tp) cc_final: 0.9347 (mp) REVERT: A 461 PHE cc_start: 0.8312 (m-80) cc_final: 0.7954 (t80) REVERT: A 486 TYR cc_start: 0.8802 (m-80) cc_final: 0.8259 (m-80) REVERT: A 1026 MET cc_start: 0.9324 (tpp) cc_final: 0.8545 (ttm) REVERT: B 133 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: B 520 THR cc_start: 0.7928 (p) cc_final: 0.7638 (p) REVERT: B 1138 LEU cc_start: 0.9180 (mp) cc_final: 0.8947 (pp) REVERT: C 58 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (m-10) REVERT: C 229 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7620 (tt) REVERT: C 350 TRP cc_start: 0.8559 (p-90) cc_final: 0.7942 (p-90) REVERT: C 399 ILE cc_start: 0.8464 (pt) cc_final: 0.8167 (pt) REVERT: C 502 TYR cc_start: 0.9045 (m-80) cc_final: 0.8802 (m-10) REVERT: C 866 MET cc_start: 0.8892 (mtm) cc_final: 0.8528 (ttm) REVERT: L 17 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8541 (mt-10) REVERT: L 33 TYR cc_start: 0.8937 (m-80) cc_final: 0.8721 (m-80) REVERT: L 80 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9013 (mm-30) REVERT: H 10 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6859 (mm-30) REVERT: H 32 TYR cc_start: 0.8754 (m-80) cc_final: 0.8221 (m-80) REVERT: H 80 TYR cc_start: 0.8758 (m-80) cc_final: 0.8220 (m-80) REVERT: F 4 MET cc_start: 0.8269 (mmm) cc_final: 0.8055 (mmm) REVERT: F 36 TRP cc_start: 0.8369 (m100) cc_final: 0.7938 (m100) REVERT: F 98 MET cc_start: 0.8435 (mpp) cc_final: 0.8156 (ptp) REVERT: E 23 LYS cc_start: 0.9202 (mttt) cc_final: 0.8959 (mppt) REVERT: E 48 MET cc_start: 0.8646 (mtp) cc_final: 0.8102 (mtp) REVERT: K 61 ASP cc_start: 0.9164 (p0) cc_final: 0.8822 (p0) REVERT: J 10 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7622 (mm-30) REVERT: J 48 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7790 (mmm) REVERT: J 107 MET cc_start: 0.8359 (mtt) cc_final: 0.7970 (mtt) outliers start: 67 outliers final: 57 residues processed: 239 average time/residue: 0.5714 time to fit residues: 215.3817 Evaluate side-chains 236 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 175 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 884 THR Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 2.9990 chunk 405 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 425 optimal weight: 8.9990 chunk 391 optimal weight: 40.0000 chunk 338 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN J 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35040 Z= 0.212 Angle : 0.526 9.427 47699 Z= 0.266 Chirality : 0.043 0.235 5610 Planarity : 0.004 0.086 6065 Dihedral : 4.981 52.155 5968 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.63 % Allowed : 11.88 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.12 (0.13), residues: 4252 helix: 1.58 (0.20), residues: 748 sheet: 0.33 (0.14), residues: 1310 loop : -0.56 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 104 HIS 0.004 0.001 HIS B1045 PHE 0.027 0.001 PHE A 389 TYR 0.030 0.001 TYR F 99 ARG 0.014 0.000 ARG F 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 183 time to evaluate : 3.776 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: A 92 PHE cc_start: 0.7770 (t80) cc_final: 0.7294 (t80) REVERT: A 118 LEU cc_start: 0.9622 (tp) cc_final: 0.9343 (mp) REVERT: A 461 PHE cc_start: 0.8240 (m-80) cc_final: 0.7886 (t80) REVERT: A 486 TYR cc_start: 0.8814 (m-80) cc_final: 0.8208 (m-80) REVERT: A 1026 MET cc_start: 0.9252 (tpp) cc_final: 0.8474 (ttm) REVERT: B 133 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: B 210 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 520 THR cc_start: 0.7783 (p) cc_final: 0.7496 (p) REVERT: C 58 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8686 (m-10) REVERT: C 229 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7437 (tt) REVERT: C 350 TRP cc_start: 0.8467 (p-90) cc_final: 0.8051 (p-90) REVERT: C 399 ILE cc_start: 0.8405 (pt) cc_final: 0.8107 (pt) REVERT: C 502 TYR cc_start: 0.9028 (m-80) cc_final: 0.8810 (m-10) REVERT: L 80 GLU cc_start: 0.9324 (mm-30) cc_final: 0.9035 (mm-30) REVERT: H 10 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6890 (mm-30) REVERT: H 32 TYR cc_start: 0.8722 (m-80) cc_final: 0.8285 (m-80) REVERT: H 80 TYR cc_start: 0.8713 (m-80) cc_final: 0.8154 (m-10) REVERT: F 4 MET cc_start: 0.8189 (mmm) cc_final: 0.7632 (mmm) REVERT: F 36 TRP cc_start: 0.8264 (m100) cc_final: 0.7713 (m100) REVERT: F 97 ARG cc_start: 0.8679 (mtp-110) cc_final: 0.8373 (mtp-110) REVERT: F 98 MET cc_start: 0.8413 (mpp) cc_final: 0.8072 (ptp) REVERT: E 48 MET cc_start: 0.8539 (mtp) cc_final: 0.7994 (mtp) REVERT: K 61 ASP cc_start: 0.9176 (p0) cc_final: 0.8823 (p0) REVERT: K 97 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8021 (mmt180) REVERT: J 10 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7643 (mm-30) REVERT: J 48 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7675 (mmm) REVERT: J 107 MET cc_start: 0.8352 (mtt) cc_final: 0.7973 (mtt) outliers start: 61 outliers final: 52 residues processed: 236 average time/residue: 0.5287 time to fit residues: 195.5888 Evaluate side-chains 232 residues out of total 3747 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 938 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 884 THR Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 48 MET Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 197 GLN Chi-restraints excluded: chain J residue 206 LYS 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: 30.0000 chunk 103 optimal weight: 2.9990 chunk 312 optimal weight: 40.0000 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.118833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078507 restraints weight = 115573.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076293 restraints weight = 72021.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076357 restraints weight = 61630.812| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 35040 Z= 0.321 Angle : 0.650 59.189 47699 Z= 0.353 Chirality : 0.045 0.687 5610 Planarity : 0.004 0.085 6065 Dihedral : 4.958 52.151 5966 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.58 % Allowed : 11.91 % Favored : 86.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.31 % 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: 0.11 (0.13), residues: 4252 helix: 1.55 (0.20), residues: 748 sheet: 0.33 (0.14), residues: 1310 loop : -0.58 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.003 0.001 HIS A 652 PHE 0.062 0.002 PHE A 133 TYR 0.037 0.001 TYR A 160 ARG 0.016 0.001 ARG L 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7404.52 seconds wall clock time: 136 minutes 33.17 seconds (8193.17 seconds total)