Starting phenix.real_space_refine on Wed Feb 21 21:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we9_32443/02_2024/7we9_32443.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we9_32443/02_2024/7we9_32443.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/7we9_32443/02_2024/7we9_32443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we9_32443/02_2024/7we9_32443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we9_32443/02_2024/7we9_32443.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7we9_32443/02_2024/7we9_32443.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= 0.000 sd= 0.073 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 138 5.16 5 C 20384 2.51 5 N 5260 2.21 5 O 6261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B GLU 1014": "OE1" <-> "OE2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 985": "OE1" <-> "OE2" Residue "F TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L ASP 86": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32043 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "F" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "D" 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: "E" 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: "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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" 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 Time building chain proxies: 16.66, per 1000 atoms: 0.52 Number of scatterers: 32043 At special positions: 0 Unit cell: (154.08, 178.69, 245.03, 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 138 16.00 O 6261 8.00 N 5260 7.00 C 20384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " 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=2.04 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 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " 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=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 129 " - pdb=" SG CYS F 161 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 298 " distance=2.03 Simple disulfide: pdb=" SG CYS F 333 " - pdb=" SG CYS F 358 " distance=2.03 Simple disulfide: pdb=" SG CYS F 376 " - pdb=" SG CYS F 429 " distance=2.03 Simple disulfide: pdb=" SG CYS F 388 " - pdb=" SG CYS F 522 " distance=2.03 Simple disulfide: pdb=" SG CYS F 477 " - pdb=" SG CYS F 485 " distance=2.03 Simple disulfide: pdb=" SG CYS F 614 " - pdb=" SG CYS F 646 " distance=2.03 Simple disulfide: pdb=" SG CYS F 659 " - pdb=" SG CYS F 668 " distance=2.03 Simple disulfide: pdb=" SG CYS F 735 " - pdb=" SG CYS F 757 " distance=2.03 Simple disulfide: pdb=" SG CYS F 740 " - pdb=" SG CYS F 746 " distance=2.03 Simple disulfide: pdb=" SG CYS F1029 " - pdb=" SG CYS F1040 " distance=2.03 Simple disulfide: pdb=" SG CYS F1079 " - pdb=" SG CYS F1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " 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=2, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " NAG-ASN " NAG A1302 " - " ASN A1155 " " NAG A1303 " - " ASN A 143 " " NAG A1304 " - " ASN A 17 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 600 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 706 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG D 1 " - " ASN A 231 " " NAG E 1 " - " ASN A 328 " " NAG F1301 " - " ASN F1155 " " NAG F1302 " - " ASN F 123 " " NAG F1303 " - " ASN F 143 " " NAG F1304 " - " ASN F 17 " " NAG F1305 " - " ASN F 61 " " NAG F1306 " - " ASN F 600 " " NAG F1307 " - " ASN F 654 " " NAG F1308 " - " ASN F 613 " " NAG F1309 " - " ASN F 706 " " NAG G 1 " - " ASN A 714 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1095 " " NAG P 1 " - " ASN A1131 " " NAG S 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN F 231 " " NAG Y 1 " - " ASN F 714 " " NAG a 1 " - " ASN F 798 " " NAG b 1 " - " ASN F1095 " " NAG c 1 " - " ASN F1131 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.79 Conformation dependent library (CDL) restraints added in 6.0 seconds 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 58 sheets defined 19.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.680A pdb=" N LEU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.589A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.103A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.804A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.640A pdb=" N GLY A 636 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.605A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 751 through 754 removed outlier: 3.661A pdb=" N GLY A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 756 through 771 removed outlier: 3.898A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 762 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 4.392A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 863 through 878 removed outlier: 3.696A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 918 through 928 removed outlier: 4.008A pdb=" N PHE A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 936 removed outlier: 4.329A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 952 removed outlier: 4.835A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 962 removed outlier: 3.528A pdb=" N ASN A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) 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 974 through 979 removed outlier: 3.561A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1016 removed outlier: 4.236A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1026 Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 3.575A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1158 removed outlier: 4.819A pdb=" N TYR A1152 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A1153 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A1156 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.522A pdb=" N LYS B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.771A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.154A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 4.208A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.849A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N LEU B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 777 removed outlier: 3.747A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 Processing helix chain 'B' and resid 847 through 851 removed outlier: 3.949A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 878 removed outlier: 3.521A pdb=" N GLY B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.593A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.520A pdb=" N MET B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.672A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 928 removed outlier: 3.832A pdb=" N PHE B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 936 removed outlier: 4.330A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.068A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (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 removed outlier: 3.915A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1019 removed outlier: 3.501A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1139 through 1153 removed outlier: 3.905A pdb=" N ASP B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B1151 " --> pdb=" O GLU B1147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1158 removed outlier: 3.824A pdb=" N THR B1157 " --> pdb=" O PHE B1153 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1153 through 1158' Processing helix chain 'F' and resid 291 through 299 Processing helix chain 'F' and resid 334 through 340 removed outlier: 4.251A pdb=" N VAL F 338 " --> pdb=" O PRO F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 Processing helix chain 'F' and resid 381 through 386 removed outlier: 3.556A pdb=" N LEU F 384 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN F 385 " --> pdb=" O THR F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 removed outlier: 3.538A pdb=" N ILE F 407 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 408 " --> pdb=" O ARG F 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 408' Processing helix chain 'F' and resid 413 through 419 removed outlier: 3.725A pdb=" N TYR F 418 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN F 419 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 621 removed outlier: 4.020A pdb=" N VAL F 619 " --> pdb=" O THR F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 3.953A pdb=" N LEU F 749 " --> pdb=" O GLU F 745 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR F 753 " --> pdb=" O LEU F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 779 removed outlier: 3.699A pdb=" N THR F 758 " --> pdb=" O GLY F 754 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 768 " --> pdb=" O LEU F 764 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU F 770 " --> pdb=" O GLY F 766 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F 772 " --> pdb=" O ALA F 768 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR F 775 " --> pdb=" O GLN F 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 777 " --> pdb=" O LYS F 773 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE F 779 " --> pdb=" O THR F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 813 through 823 Processing helix chain 'F' and resid 863 through 881 Processing helix chain 'F' and resid 882 through 885 removed outlier: 4.247A pdb=" N PHE F 885 " --> pdb=" O GLY F 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 882 through 885' Processing helix chain 'F' and resid 898 through 903 Processing helix chain 'F' and resid 904 through 906 No H-bonds generated for 'chain 'F' and resid 904 through 906' Processing helix chain 'F' and resid 911 through 916 Processing helix chain 'F' and resid 916 through 936 removed outlier: 3.732A pdb=" N ASN F 925 " --> pdb=" O ALA F 921 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 927 " --> pdb=" O GLN F 923 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE F 928 " --> pdb=" O PHE F 924 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 929 " --> pdb=" O ASN F 925 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN F 932 " --> pdb=" O ILE F 928 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP F 933 " --> pdb=" O GLY F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 942 through 962 removed outlier: 3.869A pdb=" N GLN F 946 " --> pdb=" O LEU F 942 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP F 947 " --> pdb=" O GLY F 943 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL F 948 " --> pdb=" O LYS F 944 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU F 956 " --> pdb=" O ASN F 952 " (cutoff:3.500A) Processing helix chain 'F' and resid 963 through 965 No H-bonds generated for 'chain 'F' and resid 963 through 965' Processing helix chain 'F' and resid 973 through 979 removed outlier: 3.581A pdb=" N ILE F 977 " --> pdb=" O VAL F 973 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE F 978 " --> pdb=" O LEU F 974 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER F 979 " --> pdb=" O ASN F 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 973 through 979' Processing helix chain 'F' and resid 982 through 1026 removed outlier: 4.012A pdb=" N GLU F 987 " --> pdb=" O LYS F 983 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL F 988 " --> pdb=" O VAL F 984 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 989 " --> pdb=" O GLU F 985 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU F 993 " --> pdb=" O GLN F 989 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F1004 " --> pdb=" O SER F1000 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE F1010 " --> pdb=" O THR F1006 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA F1017 " --> pdb=" O ALA F1013 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA F1023 " --> pdb=" O ALA F1019 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR F1024 " --> pdb=" O ASN F1020 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET F1026 " --> pdb=" O ALA F1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 1113 through 1115 No H-bonds generated for 'chain 'F' and resid 1113 through 1115' Processing helix chain 'F' and resid 1139 through 1157 removed outlier: 4.480A pdb=" N SER F1144 " --> pdb=" O PRO F1140 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE F1145 " --> pdb=" O GLU F1141 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS F1146 " --> pdb=" O LEU F1142 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU F1147 " --> pdb=" O ASP F1143 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU F1148 " --> pdb=" O SER F1144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F1149 " --> pdb=" O PHE F1145 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS F1151 " --> pdb=" O GLU F1147 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR F1152 " --> pdb=" O GLU F1148 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F1153 " --> pdb=" O LEU F1149 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS F1154 " --> pdb=" O ASP F1150 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F1155 " --> pdb=" O LYS F1151 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F1156 " --> pdb=" O TYR F1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.531A pdb=" N SER C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.084A pdb=" N THR C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.544A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.867A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.618A pdb=" N THR I 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.081A pdb=" N GLU K 84 " --> pdb=" O SER K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.689A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.618A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.506A pdb=" N GLN A 236 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 103 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.272A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.705A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 399 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 434 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE A 371 " --> pdb=" O ASN A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.848A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 548 through 551 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 642 removed outlier: 3.843A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.590A pdb=" N GLU A 651 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 691 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.318A pdb=" N ASN A 700 " --> pdb=" O LYS F 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.927A pdb=" N ILE A 709 " --> pdb=" O PHE A1072 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A1072 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 711 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 716 Processing sheet with id=AB5, first strand: chain 'A' and resid 719 through 725 removed outlier: 3.807A pdb=" N THR A 720 " --> pdb=" O HIS A1061 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.512A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.072A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 224 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.817A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 82 through 83 removed outlier: 4.329A pdb=" N LEU B 82 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE B 235 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 129 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.806A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AC5, first strand: chain 'B' and resid 321 through 325 removed outlier: 7.689A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 353 through 355 removed outlier: 4.202A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 509 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.686A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 521 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.507A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 562 through 564 removed outlier: 4.267A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 661 through 662 removed outlier: 3.805A pdb=" N ILE B 661 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 712 removed outlier: 3.536A pdb=" N LYS B1070 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 724 removed outlier: 3.761A pdb=" N PHE B1049 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B1062 " --> pdb=" O MET B1047 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1078 through 1079 Processing sheet with id=AD6, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD7, first strand: chain 'F' and resid 27 through 31 removed outlier: 3.805A pdb=" N SER F 60 " --> pdb=" O SER F 31 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASN F 61 " --> pdb=" O TYR F 266 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR F 266 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 261 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER F 200 " --> pdb=" O PRO F 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 48 through 55 removed outlier: 3.818A pdb=" N ASP F 284 " --> pdb=" O LYS F 275 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AE1, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.836A pdb=" N PHE F 163 " --> pdb=" O VAL F 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 308 through 316 removed outlier: 4.040A pdb=" N THR F 596 " --> pdb=" O GLY F 308 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL F 592 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN F 314 " --> pdb=" O GLY F 590 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY F 590 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 351 through 355 removed outlier: 3.837A pdb=" N ASN F 351 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 392 " --> pdb=" O ILE F 355 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 358 through 359 removed outlier: 6.752A pdb=" N CYS F 358 " --> pdb=" O CYS F 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'F' and resid 548 through 551 removed outlier: 3.640A pdb=" N VAL F 548 " --> pdb=" O THR F 585 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR F 585 " --> pdb=" O VAL F 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 651 through 652 removed outlier: 3.621A pdb=" N GLU F 651 " --> pdb=" O ILE F 689 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA F 691 " --> pdb=" O GLU F 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 688 " --> pdb=" O GLN F 672 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN F 672 " --> pdb=" O SER F 688 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA F 669 " --> pdb=" O PRO F 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 720 through 724 removed outlier: 3.702A pdb=" N MET F1047 " --> pdb=" O VAL F1062 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYR F1064 " --> pdb=" O HIS F1045 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS F1045 " --> pdb=" O TYR F1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 1073 through 1074 removed outlier: 4.034A pdb=" N THR F1073 " --> pdb=" O SER F1094 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F1094 " --> pdb=" O THR F1073 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 1117 through 1122 removed outlier: 5.193A pdb=" N ALA F1084 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS F1079 " --> pdb=" O VAL F1130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.965A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 72 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.458A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 5 through 6 removed outlier: 4.041A pdb=" N TYR H 79 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.692A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.608A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.753A pdb=" N VAL J 18 " --> pdb=" O ILE J 76 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 49 through 50 removed outlier: 4.165A pdb=" N VAL J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'K' and resid 46 through 50 removed outlier: 5.606A pdb=" N LEU K 47 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN K 38 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA K 91 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL K 102 " --> pdb=" O ALA K 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.839A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.775A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 17 through 23 849 hydrogen bonds defined for protein. 2196 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: 12.14 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10050 1.34 - 1.46: 8268 1.46 - 1.59: 14301 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 32796 Sorted by residual: bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG F1305 " pdb=" O5 NAG F1305 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 32791 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.42: 642 105.42 - 112.66: 17435 112.66 - 119.91: 10940 119.91 - 127.16: 15286 127.16 - 134.41: 323 Bond angle restraints: 44626 Sorted by residual: angle pdb=" N VAL A 617 " pdb=" CA VAL A 617 " pdb=" CB VAL A 617 " ideal model delta sigma weight residual 110.50 115.05 -4.55 6.30e-01 2.52e+00 5.22e+01 angle pdb=" N ASN F 541 " pdb=" CA ASN F 541 " pdb=" C ASN F 541 " ideal model delta sigma weight residual 110.91 118.69 -7.78 1.17e+00 7.31e-01 4.43e+01 angle pdb=" O ASP B 136 " pdb=" C ASP B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 121.37 116.10 5.27 9.00e-01 1.23e+00 3.43e+01 angle pdb=" C GLU A 321 " pdb=" N SER A 322 " pdb=" CA SER A 322 " ideal model delta sigma weight residual 122.59 113.40 9.19 1.57e+00 4.06e-01 3.42e+01 angle pdb=" CA ASP B 136 " pdb=" C ASP B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 117.75 122.57 -4.82 9.90e-01 1.02e+00 2.37e+01 ... (remaining 44621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 18983 23.84 - 47.68: 1132 47.68 - 71.52: 145 71.52 - 95.35: 79 95.35 - 119.19: 54 Dihedral angle restraints: 20393 sinusoidal: 8834 harmonic: 11559 Sorted by residual: dihedral pdb=" CA ASP F 140 " pdb=" C ASP F 140 " pdb=" N HIS F 141 " pdb=" CA HIS F 141 " ideal model delta harmonic sigma weight residual 180.00 120.75 59.25 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CB CYS F1029 " pdb=" SG CYS F1029 " pdb=" SG CYS F1040 " pdb=" CB CYS F1040 " ideal model delta sinusoidal sigma weight residual 93.00 -179.14 -87.86 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 1.73 -87.73 1 1.00e+01 1.00e-02 9.22e+01 ... (remaining 20390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 5133 0.130 - 0.260: 62 0.260 - 0.390: 8 0.390 - 0.520: 2 0.520 - 0.650: 1 Chirality restraints: 5206 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN F1131 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.11e+00 ... (remaining 5203 not shown) Planarity restraints: 5701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 789 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO F 790 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO F 790 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 790 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO L 8 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 203 " 0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO F 204 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 204 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 204 " 0.043 5.00e-02 4.00e+02 ... (remaining 5698 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 761 2.67 - 3.23: 30671 3.23 - 3.79: 45202 3.79 - 4.34: 60124 4.34 - 4.90: 97885 Nonbonded interactions: 234643 Sorted by model distance: nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.118 2.440 nonbonded pdb=" O ALA A1023 " pdb=" OG SER A1027 " model vdw 2.145 2.440 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.147 2.440 nonbonded pdb=" O ALA F 876 " pdb=" OG1 THR F 880 " model vdw 2.154 2.440 nonbonded pdb=" O GLU B 658 " pdb=" OH TYR B 692 " model vdw 2.159 2.440 ... (remaining 234638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.010 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 81.880 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 32796 Z= 0.304 Angle : 0.703 10.929 44626 Z= 0.372 Chirality : 0.051 0.650 5206 Planarity : 0.004 0.095 5659 Dihedral : 16.563 119.193 12842 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.16 % Favored : 91.71 % Rotamer: Outliers : 0.17 % Allowed : 0.58 % Favored : 99.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.16 (0.13), residues: 3945 helix: -1.90 (0.19), residues: 618 sheet: -0.36 (0.19), residues: 792 loop : -1.74 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 36 HIS 0.005 0.001 HIS A1085 PHE 0.019 0.001 PHE A1106 TYR 0.021 0.001 TYR F 377 ARG 0.007 0.000 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 261 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 THR cc_start: 0.5672 (OUTLIER) cc_final: 0.5307 (t) REVERT: A 495 ARG cc_start: 0.7529 (mmp80) cc_final: 0.7198 (mmm160) REVERT: F 52 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8059 (tm-30) REVERT: F 172 MET cc_start: 0.3554 (mmp) cc_final: 0.2720 (mpp) REVERT: F 193 ASP cc_start: 0.8569 (t70) cc_final: 0.8107 (t70) outliers start: 6 outliers final: 2 residues processed: 267 average time/residue: 0.4177 time to fit residues: 184.4131 Evaluate side-chains 213 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain B residue 672 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 120 optimal weight: 0.2980 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 359 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 314 ASN A 367 ASN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32796 Z= 0.178 Angle : 0.609 11.816 44626 Z= 0.305 Chirality : 0.047 0.389 5206 Planarity : 0.004 0.066 5659 Dihedral : 12.634 114.248 5788 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.64 % Allowed : 7.18 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.13), residues: 3945 helix: -1.36 (0.19), residues: 640 sheet: -0.25 (0.20), residues: 734 loop : -1.77 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 106 HIS 0.006 0.001 HIS F1098 PHE 0.019 0.001 PHE B1118 TYR 0.025 0.001 TYR F 704 ARG 0.005 0.000 ARG F 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 3.319 Fit side-chains revert: symmetry clash REVERT: A 320 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5257 (t) REVERT: A 495 ARG cc_start: 0.7500 (mmp80) cc_final: 0.7188 (mmm160) REVERT: F 395 ASP cc_start: 0.8336 (m-30) cc_final: 0.8036 (m-30) REVERT: F 899 MET cc_start: 0.8016 (mmt) cc_final: 0.7740 (mmp) REVERT: F 1014 GLU cc_start: 0.7258 (pt0) cc_final: 0.7034 (pt0) REVERT: I 80 MET cc_start: 0.0080 (mpp) cc_final: -0.0695 (tmm) outliers start: 22 outliers final: 12 residues processed: 240 average time/residue: 0.4060 time to fit residues: 163.3142 Evaluate side-chains 222 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 1027 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 299 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 360 optimal weight: 8.9990 chunk 389 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 chunk 357 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 951 HIS ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN A1051 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32796 Z= 0.303 Angle : 0.659 11.761 44626 Z= 0.331 Chirality : 0.049 0.407 5206 Planarity : 0.004 0.061 5659 Dihedral : 10.913 115.095 5785 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.25 % Favored : 90.67 % Rotamer: Outliers : 1.54 % Allowed : 11.60 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.21 (0.13), residues: 3945 helix: -1.47 (0.19), residues: 673 sheet: -0.45 (0.20), residues: 760 loop : -1.89 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1099 HIS 0.005 0.001 HIS A1085 PHE 0.025 0.002 PHE B1118 TYR 0.027 0.002 TYR A1064 ARG 0.004 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 224 time to evaluate : 3.524 Fit side-chains REVERT: A 495 ARG cc_start: 0.7487 (mmp80) cc_final: 0.7185 (mmm160) REVERT: A 541 ASN cc_start: 0.8033 (m-40) cc_final: 0.7311 (p0) REVERT: A 694 MET cc_start: 0.7376 (mpp) cc_final: 0.7125 (mpp) REVERT: F 148 MET cc_start: 0.3761 (mtm) cc_final: 0.3410 (ttp) REVERT: F 395 ASP cc_start: 0.8317 (m-30) cc_final: 0.8079 (m-30) REVERT: F 866 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.4498 (mtp) REVERT: C 48 MET cc_start: 0.6795 (tpp) cc_final: 0.6384 (mmm) REVERT: K 47 LEU cc_start: 0.5267 (tp) cc_final: 0.5041 (tp) REVERT: L 67 LYS cc_start: 0.8615 (mttt) cc_final: 0.8384 (mttt) outliers start: 53 outliers final: 26 residues processed: 265 average time/residue: 0.4178 time to fit residues: 184.1130 Evaluate side-chains 233 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 237 THR Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 20.0000 chunk 270 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 171 optimal weight: 0.5980 chunk 241 optimal weight: 6.9990 chunk 361 optimal weight: 30.0000 chunk 382 optimal weight: 5.9990 chunk 188 optimal weight: 0.4980 chunk 342 optimal weight: 50.0000 chunk 103 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 ASN B 672 GLN F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32796 Z= 0.283 Angle : 0.638 12.205 44626 Z= 0.319 Chirality : 0.048 0.408 5206 Planarity : 0.004 0.058 5659 Dihedral : 9.806 113.467 5784 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.06 % Favored : 91.84 % Rotamer: Outliers : 2.18 % Allowed : 14.09 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 3945 helix: -1.36 (0.19), residues: 662 sheet: -0.58 (0.20), residues: 756 loop : -1.90 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1099 HIS 0.005 0.001 HIS A1085 PHE 0.022 0.002 PHE B1118 TYR 0.024 0.002 TYR A1064 ARG 0.004 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 222 time to evaluate : 3.663 Fit side-chains REVERT: A 495 ARG cc_start: 0.7333 (mmp80) cc_final: 0.7133 (mmm160) REVERT: A 541 ASN cc_start: 0.8072 (m-40) cc_final: 0.7309 (p0) REVERT: A 874 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6828 (mm) REVERT: F 148 MET cc_start: 0.3740 (mtm) cc_final: 0.3325 (ttp) REVERT: F 172 MET cc_start: 0.3438 (mmp) cc_final: 0.2605 (mpp) REVERT: F 395 ASP cc_start: 0.8290 (m-30) cc_final: 0.8082 (m-30) REVERT: F 895 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7079 (t80) REVERT: F 1010 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8464 (mt) REVERT: C 48 MET cc_start: 0.6561 (tpp) cc_final: 0.6235 (mmm) REVERT: K 47 LEU cc_start: 0.5389 (tp) cc_final: 0.5138 (tp) REVERT: L 67 LYS cc_start: 0.8609 (mttt) cc_final: 0.8338 (mttt) outliers start: 75 outliers final: 46 residues processed: 288 average time/residue: 0.4014 time to fit residues: 194.5336 Evaluate side-chains 253 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 204 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 52 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 4.9990 chunk 217 optimal weight: 0.0370 chunk 5 optimal weight: 7.9990 chunk 285 optimal weight: 0.4980 chunk 157 optimal weight: 0.7980 chunk 326 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 343 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 overall best weight: 1.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32796 Z= 0.212 Angle : 0.605 11.506 44626 Z= 0.300 Chirality : 0.047 0.394 5206 Planarity : 0.004 0.058 5659 Dihedral : 9.023 112.434 5784 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 2.59 % Allowed : 14.82 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3945 helix: -1.12 (0.20), residues: 656 sheet: -0.51 (0.19), residues: 762 loop : -1.86 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 101 HIS 0.004 0.001 HIS A1085 PHE 0.033 0.001 PHE F 538 TYR 0.018 0.001 TYR F 704 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 213 time to evaluate : 3.505 Fit side-chains REVERT: A 495 ARG cc_start: 0.7297 (mmp80) cc_final: 0.7085 (mmm160) REVERT: A 541 ASN cc_start: 0.8059 (m-40) cc_final: 0.7272 (p0) REVERT: A 874 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6560 (mm) REVERT: F 148 MET cc_start: 0.3953 (mtm) cc_final: 0.3472 (ttp) REVERT: F 981 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7970 (pp) REVERT: F 1010 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8443 (mt) REVERT: C 80 MET cc_start: 0.3763 (ttm) cc_final: 0.3317 (ttm) REVERT: C 81 GLU cc_start: 0.7360 (tt0) cc_final: 0.7153 (mp0) REVERT: I 48 MET cc_start: 0.3993 (mtm) cc_final: 0.2238 (tmm) REVERT: K 47 LEU cc_start: 0.5376 (tp) cc_final: 0.5123 (tp) outliers start: 89 outliers final: 58 residues processed: 292 average time/residue: 0.4080 time to fit residues: 199.0294 Evaluate side-chains 268 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 207 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain B residue 1106 PHE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 866 MET Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 981 LEU Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain L residue 52 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.9990 chunk 344 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 383 optimal weight: 0.9980 chunk 318 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 32796 Z= 0.188 Angle : 0.592 12.276 44626 Z= 0.293 Chirality : 0.046 0.388 5206 Planarity : 0.004 0.059 5659 Dihedral : 8.418 110.779 5783 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.15 % Favored : 92.75 % Rotamer: Outliers : 2.47 % Allowed : 15.69 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3945 helix: -0.96 (0.20), residues: 653 sheet: -0.47 (0.19), residues: 768 loop : -1.82 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 101 HIS 0.004 0.001 HIS F1098 PHE 0.029 0.001 PHE F 538 TYR 0.016 0.001 TYR F 704 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 225 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 ARG cc_start: 0.7327 (mmp80) cc_final: 0.7089 (mmm160) REVERT: A 541 ASN cc_start: 0.8046 (m-40) cc_final: 0.7288 (p0) REVERT: A 874 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6555 (mm) REVERT: F 148 MET cc_start: 0.3963 (mtm) cc_final: 0.3481 (ttp) REVERT: F 172 MET cc_start: 0.3621 (mmp) cc_final: 0.2813 (mpp) REVERT: F 704 TYR cc_start: 0.6882 (t80) cc_final: 0.6521 (t80) REVERT: F 981 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7995 (pp) REVERT: F 1010 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 80 MET cc_start: 0.4530 (ttm) cc_final: 0.3687 (ttp) REVERT: I 48 MET cc_start: 0.4155 (mtm) cc_final: 0.2405 (tmm) REVERT: K 47 LEU cc_start: 0.5368 (tp) cc_final: 0.5123 (tp) outliers start: 85 outliers final: 59 residues processed: 297 average time/residue: 0.4065 time to fit residues: 203.9795 Evaluate side-chains 272 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 981 LEU Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1091 VAL Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 218 optimal weight: 40.0000 chunk 279 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 322 optimal weight: 0.0010 chunk 213 optimal weight: 0.4980 chunk 381 optimal weight: 50.0000 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN F 113 GLN ** F 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32796 Z= 0.164 Angle : 0.574 12.075 44626 Z= 0.284 Chirality : 0.046 0.381 5206 Planarity : 0.004 0.057 5659 Dihedral : 7.841 107.930 5783 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.08 % Rotamer: Outliers : 2.27 % Allowed : 16.39 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3945 helix: -0.72 (0.20), residues: 650 sheet: -0.30 (0.20), residues: 744 loop : -1.78 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 36 HIS 0.003 0.001 HIS F1098 PHE 0.017 0.001 PHE B 43 TYR 0.016 0.001 TYR F 704 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7995 (m-40) cc_final: 0.7262 (p0) REVERT: A 874 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6657 (mm) REVERT: F 148 MET cc_start: 0.3830 (mtm) cc_final: 0.3369 (ttp) REVERT: F 704 TYR cc_start: 0.6893 (t80) cc_final: 0.6545 (t80) REVERT: F 1010 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8394 (mt) REVERT: I 48 MET cc_start: 0.4311 (mtm) cc_final: 0.2424 (tmm) REVERT: K 47 LEU cc_start: 0.5300 (tp) cc_final: 0.5049 (tp) outliers start: 78 outliers final: 62 residues processed: 292 average time/residue: 0.4026 time to fit residues: 197.1487 Evaluate side-chains 272 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 208 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 300 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 952 ASN ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32796 Z= 0.229 Angle : 0.602 12.503 44626 Z= 0.300 Chirality : 0.046 0.388 5206 Planarity : 0.004 0.054 5659 Dihedral : 7.675 103.935 5783 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.98 % Favored : 91.91 % Rotamer: Outliers : 2.50 % Allowed : 16.86 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3945 helix: -0.76 (0.20), residues: 651 sheet: -0.43 (0.20), residues: 758 loop : -1.78 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 36 HIS 0.004 0.001 HIS A1061 PHE 0.029 0.001 PHE F 187 TYR 0.021 0.001 TYR B 165 ARG 0.005 0.000 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 212 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.8029 (m-40) cc_final: 0.7257 (p0) REVERT: A 874 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6607 (mm) REVERT: F 148 MET cc_start: 0.3844 (mtm) cc_final: 0.3369 (ttp) REVERT: F 172 MET cc_start: 0.3404 (mmp) cc_final: 0.2742 (mpp) REVERT: F 539 ASN cc_start: -0.2568 (OUTLIER) cc_final: -0.2881 (p0) REVERT: F 704 TYR cc_start: 0.6984 (t80) cc_final: 0.6634 (t80) REVERT: F 1010 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8413 (mt) REVERT: I 48 MET cc_start: 0.4419 (mtm) cc_final: 0.4064 (mtm) REVERT: K 47 LEU cc_start: 0.5204 (tp) cc_final: 0.4975 (tp) outliers start: 86 outliers final: 74 residues processed: 289 average time/residue: 0.3951 time to fit residues: 194.7927 Evaluate side-chains 279 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 202 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1091 VAL Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 154 optimal weight: 0.1980 chunk 279 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 321 optimal weight: 0.8980 chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32796 Z= 0.245 Angle : 0.616 12.564 44626 Z= 0.308 Chirality : 0.047 0.383 5206 Planarity : 0.004 0.058 5659 Dihedral : 7.498 97.630 5783 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.26 % Favored : 91.63 % Rotamer: Outliers : 2.62 % Allowed : 17.35 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3945 helix: -0.83 (0.20), residues: 659 sheet: -0.36 (0.19), residues: 775 loop : -1.84 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 36 HIS 0.004 0.001 HIS A1061 PHE 0.024 0.001 PHE F 187 TYR 0.019 0.001 TYR A1064 ARG 0.004 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 213 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.8143 (m-40) cc_final: 0.7314 (p0) REVERT: A 874 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6637 (mm) REVERT: B 108 LEU cc_start: 0.5441 (mp) cc_final: 0.4787 (tp) REVERT: F 148 MET cc_start: 0.3946 (mtm) cc_final: 0.3397 (ttp) REVERT: F 172 MET cc_start: 0.3440 (mmp) cc_final: 0.2880 (mpp) REVERT: F 539 ASN cc_start: -0.2586 (OUTLIER) cc_final: -0.2921 (p0) REVERT: F 704 TYR cc_start: 0.7058 (t80) cc_final: 0.6639 (t80) REVERT: F 711 ILE cc_start: 0.5077 (OUTLIER) cc_final: 0.4833 (mm) REVERT: F 897 MET cc_start: 0.4524 (ptt) cc_final: 0.4252 (ptp) REVERT: F 1010 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8434 (mt) REVERT: I 48 MET cc_start: 0.4328 (mtm) cc_final: 0.2503 (tmm) REVERT: K 47 LEU cc_start: 0.5195 (tp) cc_final: 0.4969 (tp) outliers start: 90 outliers final: 80 residues processed: 292 average time/residue: 0.4082 time to fit residues: 202.5696 Evaluate side-chains 288 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 204 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 711 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 960 VAL Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1091 VAL Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 8.9990 chunk 376 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 394 optimal weight: 8.9990 chunk 363 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 904 ASN F 113 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 32796 Z= 0.302 Angle : 0.661 12.471 44626 Z= 0.332 Chirality : 0.048 0.394 5206 Planarity : 0.004 0.064 5659 Dihedral : 7.532 91.092 5783 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.51 % Favored : 90.39 % Rotamer: Outliers : 2.82 % Allowed : 17.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.13), residues: 3945 helix: -1.00 (0.20), residues: 657 sheet: -0.46 (0.19), residues: 804 loop : -1.91 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 36 HIS 0.005 0.001 HIS A1085 PHE 0.034 0.002 PHE B 43 TYR 0.026 0.002 TYR A1064 ARG 0.006 0.000 ARG B 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7890 Ramachandran restraints generated. 3945 Oldfield, 0 Emsley, 3945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 208 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.8146 (m-40) cc_final: 0.7239 (p0) REVERT: A 874 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6739 (mm) REVERT: B 108 LEU cc_start: 0.5527 (mp) cc_final: 0.4916 (tp) REVERT: B 315 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7288 (t80) REVERT: F 148 MET cc_start: 0.4086 (mtm) cc_final: 0.3490 (ttp) REVERT: F 172 MET cc_start: 0.3684 (mmp) cc_final: 0.2356 (mmt) REVERT: F 395 ASP cc_start: 0.8533 (m-30) cc_final: 0.8129 (m-30) REVERT: F 704 TYR cc_start: 0.6769 (t80) cc_final: 0.6375 (t80) REVERT: F 711 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4997 (mm) REVERT: F 897 MET cc_start: 0.4690 (ptt) cc_final: 0.4456 (ptp) REVERT: F 1010 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8503 (mt) REVERT: C 10 GLU cc_start: 0.8385 (pm20) cc_final: 0.8182 (pm20) REVERT: I 48 MET cc_start: 0.4494 (mtm) cc_final: 0.2726 (tmm) REVERT: K 47 LEU cc_start: 0.5258 (tp) cc_final: 0.5050 (tp) outliers start: 97 outliers final: 80 residues processed: 295 average time/residue: 0.4198 time to fit residues: 209.9364 Evaluate side-chains 288 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 204 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 916 ASN Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 735 CYS Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 885 PHE Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1091 VAL Chi-restraints excluded: chain F residue 195 TYR Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 539 ASN Chi-restraints excluded: chain F residue 548 VAL Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 632 VAL Chi-restraints excluded: chain F residue 661 ILE Chi-restraints excluded: chain F residue 663 ILE Chi-restraints excluded: chain F residue 711 ILE Chi-restraints excluded: chain F residue 814 PHE Chi-restraints excluded: chain F residue 856 THR Chi-restraints excluded: chain F residue 895 PHE Chi-restraints excluded: chain F residue 906 ILE Chi-restraints excluded: chain F residue 913 LEU Chi-restraints excluded: chain F residue 931 ILE Chi-restraints excluded: chain F residue 960 VAL Chi-restraints excluded: chain F residue 1010 ILE Chi-restraints excluded: chain F residue 1027 SER Chi-restraints excluded: chain F residue 1063 THR Chi-restraints excluded: chain F residue 1091 VAL Chi-restraints excluded: chain F residue 1126 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.8980 chunk 334 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 289 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 314 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 323 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 904 ASN B 910 GLN F 113 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.173600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.145629 restraints weight = 77677.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.141883 restraints weight = 85999.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143077 restraints weight = 70543.527| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32796 Z= 0.170 Angle : 0.597 12.109 44626 Z= 0.297 Chirality : 0.046 0.393 5206 Planarity : 0.004 0.055 5659 Dihedral : 7.122 87.690 5783 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.77 % Favored : 93.13 % Rotamer: Outliers : 2.41 % Allowed : 17.87 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -1.93 (0.13), residues: 3945 helix: -0.73 (0.20), residues: 659 sheet: -0.45 (0.20), residues: 759 loop : -1.79 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 36 HIS 0.004 0.001 HIS F1098 PHE 0.035 0.001 PHE B 43 TYR 0.019 0.001 TYR A 704 ARG 0.005 0.000 ARG F 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5764.93 seconds wall clock time: 106 minutes 48.87 seconds (6408.87 seconds total)