Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:14:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/12_2022/7akj_11813_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C GLU 762": "OE1" <-> "OE2" Residue "C GLU 801": "OE1" <-> "OE2" Residue "C PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 977": "NH1" <-> "NH2" Residue "C GLU 1013": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B GLU 762": "OE1" <-> "OE2" Residue "B GLU 801": "OE1" <-> "OE2" Residue "B PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 977": "NH1" <-> "NH2" Residue "B GLU 1013": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "L GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "B" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "N" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "T" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 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 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 chiralities: 2 Chain: "Z" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.72, per 1000 atoms: 0.49 Number of scatterers: 31812 At special positions: 0 Unit cell: (160.92, 163.08, 183.6, 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 156 16.00 O 6318 8.00 N 5127 7.00 C 20211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.05 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 6 " - " MAN N 7 " " MAN T 6 " - " MAN T 7 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " MAN N 6 " - " MAN N 8 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " MAN T 6 " - " MAN T 8 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 8 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA T 3 " - " MAN T 6 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 9 " " NAG Q 1 " - " FUC Q 3 " " NAG T 1 " - " FUC T 9 " " NAG W 1 " - " FUC W 3 " " NAG Z 1 " - " FUC Z 9 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 318 " " NAG A1305 " - " ASN A 357 " " NAG A1308 " - " ASN A 691 " " NAG A1309 " - " ASN A 699 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A1080 " " NAG A1312 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1303 " - " ASN B 158 " " NAG B1304 " - " ASN B 318 " " NAG B1305 " - " ASN B 357 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 699 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B1080 " " NAG B1312 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1303 " - " ASN C 158 " " NAG C1304 " - " ASN C 318 " " NAG C1305 " - " ASN C 357 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C1080 " " NAG C1312 " - " ASN C1116 " " NAG I 1 " - " ASN C 109 " " NAG J 1 " - " ASN C 119 " " NAG K 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 269 " " NAG N 1 " - " ASN C 330 " " NAG O 1 " - " ASN C 783 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 227 " " NAG S 1 " - " ASN B 269 " " NAG T 1 " - " ASN B 330 " " NAG U 1 " - " ASN B 783 " " NAG V 1 " - " ASN A 109 " " NAG W 1 " - " ASN A 119 " " NAG X 1 " - " ASN A 227 " " NAG Y 1 " - " ASN A 269 " " NAG Z 1 " - " ASN A 330 " " NAG a 1 " - " ASN A 783 " Time building additional restraints: 12.84 Conformation dependent library (CDL) restraints added in 4.7 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 66 sheets defined 22.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.611A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.850A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.794A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.831A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY C 871 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 895 through 901' Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.806A pdb=" N ILE C 905 " --> pdb=" O ASN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.570A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1107 through 1111 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.613A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR B 723 " --> pdb=" O ASP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.524A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 removed outlier: 4.028A pdb=" N ALA B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 901' Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE B 905 " --> pdb=" O ASN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.812A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.714A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.612A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 886 " --> pdb=" O MET A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.327A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 901' Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU C 184 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ASN C 135 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR C 150 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE C 137 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR C 148 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 113 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 117 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 124 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 302 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 422 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 363 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 441 removed outlier: 6.155A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C1029 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1076 through 1079 Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.581A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 152 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR B 150 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE B 137 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR B 148 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 117 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 124 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 302 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.745A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 422 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 363 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR B 436 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE B 483 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 438 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1029 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.990A pdb=" N CYS G 95 " --> pdb=" O TRP G 111 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP G 111 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG G 97 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS E 95 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP E 111 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG E 97 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.501A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 184 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE A 137 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR A 148 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 236 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 98 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 117 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.679A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 422 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 363 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AF8, first strand: chain 'A' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR A 436 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 483 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.721A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.268A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.700A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA A1037 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A1029 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AG4, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AG5, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.93 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9939 1.35 - 1.48: 8879 1.48 - 1.61: 13525 1.61 - 1.73: 3 1.73 - 1.86: 210 Bond restraints: 32556 Sorted by residual: bond pdb=" C1 MAN N 5 " pdb=" C2 MAN N 5 " ideal model delta sigma weight residual 1.542 1.629 -0.087 3.60e-02 7.72e+02 5.87e+00 bond pdb=" C1 MAN Z 5 " pdb=" C2 MAN Z 5 " ideal model delta sigma weight residual 1.542 1.629 -0.087 3.60e-02 7.72e+02 5.85e+00 bond pdb=" C1 MAN T 5 " pdb=" C2 MAN T 5 " ideal model delta sigma weight residual 1.542 1.629 -0.087 3.60e-02 7.72e+02 5.80e+00 bond pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.406 1.488 -0.082 3.40e-02 8.65e+02 5.80e+00 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.406 1.488 -0.082 3.40e-02 8.65e+02 5.75e+00 ... (remaining 32551 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.48: 725 105.48 - 112.61: 17083 112.61 - 119.74: 10167 119.74 - 126.88: 15978 126.88 - 134.01: 372 Bond angle restraints: 44325 Sorted by residual: angle pdb=" CA CYS B 635 " pdb=" CB CYS B 635 " pdb=" SG CYS B 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS A 635 " pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS C 635 " pdb=" CB CYS C 635 " pdb=" SG CYS C 635 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" C2 NAG C1308 " pdb=" N2 NAG C1308 " pdb=" C7 NAG C1308 " ideal model delta sigma weight residual 123.12 129.37 -6.25 1.28e+00 6.08e-01 2.37e+01 angle pdb=" C2 NAG B1308 " pdb=" N2 NAG B1308 " pdb=" C7 NAG B1308 " ideal model delta sigma weight residual 123.12 129.29 -6.17 1.28e+00 6.08e-01 2.31e+01 ... (remaining 44320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 18457 23.20 - 46.40: 629 46.40 - 69.60: 82 69.60 - 92.80: 74 92.80 - 116.00: 12 Dihedral angle restraints: 19254 sinusoidal: 7845 harmonic: 11409 Sorted by residual: dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.50 -88.50 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 19251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 5235 0.215 - 0.430: 18 0.430 - 0.644: 6 0.644 - 0.859: 3 0.859 - 1.074: 3 Chirality restraints: 5265 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 119 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 119 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 119 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.86e+01 ... (remaining 5262 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 119 " -0.047 2.00e-02 2.50e+03 4.73e-02 2.79e+01 pdb=" CG ASN B 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 119 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 119 " -0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN A 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 119 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 119 " 0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN C 119 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 119 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 119 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.054 2.00e-02 2.50e+03 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 852 2.69 - 3.25: 30936 3.25 - 3.80: 43714 3.80 - 4.35: 57195 4.35 - 4.90: 97605 Nonbonded interactions: 230302 Sorted by model distance: nonbonded pdb=" OG1 THR C 693 " pdb=" OE1 GLN A 877 " model vdw 2.143 2.440 nonbonded pdb=" OE1 GLN B 877 " pdb=" OG1 THR A 693 " model vdw 2.147 2.440 nonbonded pdb=" OE1 GLN C 877 " pdb=" OG1 THR B 693 " model vdw 2.153 2.440 nonbonded pdb=" O2 MAN T 4 " pdb=" O5 MAN T 5 " model vdw 2.161 2.440 nonbonded pdb=" O2 MAN Z 4 " pdb=" O5 MAN Z 5 " model vdw 2.162 2.440 ... (remaining 230297 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 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 20211 2.51 5 N 5127 2.21 5 O 6318 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.650 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: 15.460 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.250 Process input model: 80.200 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.087 32556 Z= 0.297 Angle : 0.829 11.741 44325 Z= 0.471 Chirality : 0.066 1.074 5265 Planarity : 0.005 0.080 5577 Dihedral : 13.192 116.000 11781 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.12), residues: 3888 helix: -1.38 (0.18), residues: 657 sheet: 0.66 (0.16), residues: 939 loop : -1.06 (0.11), residues: 2292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3816 time to fit residues: 197.1250 Evaluate side-chains 212 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 32556 Z= 0.286 Angle : 0.713 11.468 44325 Z= 0.390 Chirality : 0.054 0.549 5265 Planarity : 0.005 0.054 5577 Dihedral : 9.860 109.909 4887 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 3888 helix: 0.40 (0.20), residues: 654 sheet: 1.11 (0.18), residues: 825 loop : -0.89 (0.12), residues: 2409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 4.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 34 residues processed: 270 average time/residue: 0.3871 time to fit residues: 176.6083 Evaluate side-chains 257 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2617 time to fit residues: 21.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 354 optimal weight: 0.5980 chunk 383 optimal weight: 8.9990 chunk 315 optimal weight: 0.0270 chunk 351 optimal weight: 6.9990 chunk 120 optimal weight: 0.0670 chunk 284 optimal weight: 1.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN A 70 HIS ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 32556 Z= 0.224 Angle : 0.632 10.473 44325 Z= 0.345 Chirality : 0.052 0.533 5265 Planarity : 0.004 0.043 5577 Dihedral : 9.607 110.047 4887 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 3888 helix: 0.94 (0.21), residues: 654 sheet: 1.34 (0.18), residues: 825 loop : -0.89 (0.12), residues: 2409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 250 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 268 average time/residue: 0.3897 time to fit residues: 176.6871 Evaluate side-chains 220 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 211 time to evaluate : 3.516 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3403 time to fit residues: 10.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8963 > 50: distance: 52 - 56: 14.872 distance: 56 - 57: 22.536 distance: 57 - 58: 13.136 distance: 57 - 60: 29.942 distance: 58 - 59: 14.939 distance: 58 - 65: 28.409 distance: 60 - 61: 26.727 distance: 61 - 62: 20.267 distance: 62 - 63: 12.436 distance: 62 - 64: 12.745 distance: 65 - 66: 33.472 distance: 66 - 67: 9.139 distance: 66 - 69: 12.304 distance: 67 - 68: 26.251 distance: 67 - 74: 18.373 distance: 69 - 70: 19.544 distance: 70 - 71: 4.150 distance: 74 - 75: 16.690 distance: 75 - 76: 4.646 distance: 75 - 78: 15.233 distance: 76 - 77: 16.038 distance: 76 - 85: 13.805 distance: 78 - 79: 21.739 distance: 79 - 80: 10.516 distance: 80 - 81: 3.535 distance: 85 - 86: 14.947 distance: 86 - 87: 23.094 distance: 86 - 89: 6.048 distance: 87 - 88: 16.364 distance: 87 - 93: 25.474 distance: 89 - 90: 11.907 distance: 90 - 91: 10.104 distance: 90 - 92: 12.493 distance: 92 - 212: 12.492 distance: 93 - 94: 9.485 distance: 94 - 95: 6.111 distance: 94 - 97: 11.220 distance: 95 - 96: 15.117 distance: 95 - 104: 17.180 distance: 97 - 98: 9.469 distance: 98 - 99: 5.714 distance: 98 - 100: 5.469 distance: 99 - 101: 5.670 distance: 100 - 102: 7.402 distance: 101 - 103: 3.742 distance: 104 - 105: 17.603 distance: 105 - 106: 24.276 distance: 105 - 108: 22.045 distance: 106 - 107: 16.837 distance: 106 - 111: 34.084 distance: 108 - 109: 26.404 distance: 108 - 110: 32.184 distance: 111 - 112: 20.353 distance: 112 - 113: 7.904 distance: 112 - 115: 31.198 distance: 113 - 114: 26.619 distance: 113 - 118: 11.932 distance: 115 - 116: 49.054 distance: 115 - 117: 39.604 distance: 118 - 119: 19.125 distance: 119 - 120: 38.526 distance: 119 - 122: 54.896 distance: 120 - 121: 16.899 distance: 120 - 123: 31.499 distance: 123 - 124: 22.109 distance: 123 - 129: 43.013 distance: 124 - 125: 21.675 distance: 124 - 127: 34.097 distance: 125 - 126: 8.804 distance: 125 - 130: 36.150 distance: 127 - 128: 23.309 distance: 128 - 129: 10.012 distance: 130 - 131: 9.073 distance: 131 - 132: 35.701 distance: 131 - 134: 14.436 distance: 132 - 133: 40.621 distance: 132 - 135: 18.187