Starting phenix.real_space_refine on Fri Mar 22 01:23:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/03_2024/7akj_11813_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/03_2024/7akj_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_11813/03_2024/7akj_11813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/03_2024/7akj_11813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/03_2024/7akj_11813_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7akj_11813/03_2024/7akj_11813_neut.pdb" } resolution = 3.8 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= 0.002 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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: 9 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 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: 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: 27 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: 27 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: 27 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 dihedrals: 6 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 dihedrals: 36 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 dihedrals: 36 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 dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 16.11, per 1000 atoms: 0.51 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: 13.18 Conformation dependent library (CDL) restraints added in 6.0 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: 5.00 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: 16.29 Time building geometry restraints manager: 14.00 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 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN Z 5 " pdb=" C2 MAN Z 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN T 5 " pdb=" C2 MAN T 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (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=" CA CYS B 720 " pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " ideal model delta sigma weight residual 114.40 125.27 -10.87 2.30e+00 1.89e-01 2.23e+01 angle pdb=" CA CYS A 720 " pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " ideal model delta sigma weight residual 114.40 125.25 -10.85 2.30e+00 1.89e-01 2.23e+01 ... (remaining 44320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 19434 23.51 - 47.03: 702 47.03 - 70.54: 219 70.54 - 94.05: 123 94.05 - 117.56: 66 Dihedral angle restraints: 20544 sinusoidal: 9135 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 20541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 5226 0.215 - 0.430: 27 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 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: 4.920 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: 14.860 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 87.890 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.103 32556 Z= 0.333 Angle : 0.889 11.741 44325 Z= 0.467 Chirality : 0.068 1.074 5265 Planarity : 0.005 0.080 5577 Dihedral : 16.704 117.563 13071 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 % Allowed : 0.35 % Favored : 99.56 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 245 HIS 0.006 0.001 HIS C1030 PHE 0.045 0.002 PHE A 130 TYR 0.027 0.002 TYR H 52 ARG 0.023 0.003 ARG B 232 *********************** 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 : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.6983 (mmt) cc_final: 0.6129 (mmt) REVERT: G 52 TYR cc_start: 0.8014 (p90) cc_final: 0.7796 (p90) REVERT: A 151 MET cc_start: 0.6931 (mmt) cc_final: 0.6274 (mmt) REVERT: H 14 PRO cc_start: 0.2936 (Cg_endo) cc_final: 0.2350 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3862 time to fit residues: 198.1940 Evaluate side-chains 212 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.609 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32556 Z= 0.272 Angle : 0.789 12.797 44325 Z= 0.391 Chirality : 0.055 0.521 5265 Planarity : 0.005 0.053 5577 Dihedral : 13.391 82.846 6177 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.30 % Allowed : 5.18 % Favored : 93.52 % 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: -0.30 (0.13), residues: 3888 helix: 0.45 (0.20), residues: 654 sheet: 1.13 (0.18), residues: 831 loop : -0.90 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 245 HIS 0.005 0.001 HIS B1030 PHE 0.019 0.002 PHE C 130 TYR 0.024 0.002 TYR C1049 ARG 0.008 0.001 ARG A 747 *********************** 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 290 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7987 (mpp) cc_final: 0.7625 (mpp) REVERT: B 130 PHE cc_start: 0.5884 (m-10) cc_final: 0.5546 (m-10) REVERT: B 144 MET cc_start: 0.7894 (mpp) cc_final: 0.7646 (mpp) REVERT: B 151 MET cc_start: 0.7123 (mmt) cc_final: 0.6289 (mmt) REVERT: D 18 ARG cc_start: 0.6654 (ptm160) cc_final: 0.6436 (ptm160) REVERT: A 144 MET cc_start: 0.8004 (mpp) cc_final: 0.7325 (mpp) outliers start: 44 outliers final: 31 residues processed: 271 average time/residue: 0.3958 time to fit residues: 181.4528 Evaluate side-chains 253 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE 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: 5.9990 chunk 294 optimal weight: 6.9990 chunk 241 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 284 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 32556 Z= 0.346 Angle : 0.774 11.152 44325 Z= 0.390 Chirality : 0.056 0.530 5265 Planarity : 0.005 0.044 5577 Dihedral : 11.312 64.939 6177 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.09 % Allowed : 7.71 % Favored : 90.19 % 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: -0.46 (0.13), residues: 3888 helix: 0.67 (0.21), residues: 654 sheet: 1.04 (0.17), residues: 846 loop : -1.15 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 423 HIS 0.006 0.001 HIS C1046 PHE 0.021 0.002 PHE C 483 TYR 0.025 0.002 TYR C1049 ARG 0.008 0.001 ARG A1021 *********************** 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 303 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 232 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.8026 (mpp) cc_final: 0.7742 (mpp) REVERT: C 151 MET cc_start: 0.7205 (mmt) cc_final: 0.6958 (mmt) REVERT: C 884 MET cc_start: 0.8913 (mmp) cc_final: 0.8248 (mmt) REVERT: C 1045 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8370 (pp) REVERT: B 130 PHE cc_start: 0.6375 (m-10) cc_final: 0.5984 (m-10) REVERT: B 144 MET cc_start: 0.7968 (mpp) cc_final: 0.7766 (mpp) REVERT: B 151 MET cc_start: 0.7255 (mmt) cc_final: 0.6580 (mmt) REVERT: B 1045 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8361 (pp) REVERT: G 38 ARG cc_start: 0.7507 (ptt-90) cc_final: 0.7262 (ptt-90) REVERT: E 50 TYR cc_start: 0.8194 (p90) cc_final: 0.7980 (p90) outliers start: 71 outliers final: 47 residues processed: 275 average time/residue: 0.3864 time to fit residues: 178.7911 Evaluate side-chains 259 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 184 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 238 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 186 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 101 optimal weight: 0.3980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS C 756 GLN H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32556 Z= 0.207 Angle : 0.674 10.292 44325 Z= 0.332 Chirality : 0.052 0.520 5265 Planarity : 0.004 0.038 5577 Dihedral : 10.284 59.804 6177 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.36 % Allowed : 9.95 % Favored : 87.69 % 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: -0.34 (0.13), residues: 3888 helix: 1.00 (0.21), residues: 654 sheet: 1.07 (0.18), residues: 840 loop : -1.13 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 245 HIS 0.004 0.001 HIS C1030 PHE 0.019 0.002 PHE C 483 TYR 0.017 0.001 TYR C1049 ARG 0.004 0.000 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 4 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 310 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 230 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7938 (mpp) cc_final: 0.7719 (mpp) REVERT: C 884 MET cc_start: 0.8872 (mmp) cc_final: 0.8387 (mmt) REVERT: C 1045 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 130 PHE cc_start: 0.6325 (m-10) cc_final: 0.5969 (m-10) REVERT: B 151 MET cc_start: 0.7432 (mmt) cc_final: 0.6718 (mmt) REVERT: B 1045 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8317 (pp) REVERT: G 38 ARG cc_start: 0.7455 (ptt-90) cc_final: 0.7207 (ptt-90) REVERT: E 38 ARG cc_start: 0.7418 (ptt180) cc_final: 0.6961 (ptt-90) REVERT: E 50 TYR cc_start: 0.8168 (p90) cc_final: 0.7879 (p90) REVERT: E 100 LEU cc_start: 0.9127 (tp) cc_final: 0.8865 (tt) REVERT: A 144 MET cc_start: 0.7886 (mpp) cc_final: 0.7310 (mpp) REVERT: A 319 ILE cc_start: 0.8128 (mp) cc_final: 0.7912 (mp) outliers start: 80 outliers final: 47 residues processed: 284 average time/residue: 0.3934 time to fit residues: 188.3364 Evaluate side-chains 255 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 321 optimal weight: 0.0270 chunk 260 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 338 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 32556 Z= 0.345 Angle : 0.760 11.800 44325 Z= 0.379 Chirality : 0.056 0.522 5265 Planarity : 0.005 0.038 5577 Dihedral : 9.891 59.883 6177 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.33 % Allowed : 10.07 % Favored : 86.60 % 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: -0.67 (0.13), residues: 3888 helix: 0.77 (0.21), residues: 654 sheet: 0.90 (0.18), residues: 849 loop : -1.38 (0.11), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 245 HIS 0.005 0.001 HIS C1046 PHE 0.019 0.002 PHE A 89 TYR 0.025 0.002 TYR C1049 ARG 0.007 0.001 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 5 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 333 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 220 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 770 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7253 (mtm) REVERT: C 884 MET cc_start: 0.8865 (mmp) cc_final: 0.8400 (mmt) REVERT: C 1045 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8417 (pp) REVERT: B 130 PHE cc_start: 0.6488 (m-10) cc_final: 0.6149 (m-10) REVERT: B 144 MET cc_start: 0.7727 (mpp) cc_final: 0.7109 (mpp) REVERT: B 151 MET cc_start: 0.7376 (mmt) cc_final: 0.6690 (mmt) REVERT: B 295 ILE cc_start: 0.8710 (mp) cc_final: 0.8447 (mm) REVERT: B 1045 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8431 (pp) REVERT: G 64 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5678 (pttp) REVERT: E 38 ARG cc_start: 0.7610 (ptt180) cc_final: 0.7252 (ptt-90) REVERT: E 50 TYR cc_start: 0.8175 (p90) cc_final: 0.7937 (p90) REVERT: E 64 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5629 (pttp) REVERT: A 144 MET cc_start: 0.7912 (mpp) cc_final: 0.7480 (mpp) REVERT: A 195 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.7225 (m-10) REVERT: H 64 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.5688 (pttp) outliers start: 113 outliers final: 76 residues processed: 304 average time/residue: 0.3861 time to fit residues: 197.4306 Evaluate side-chains 290 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 207 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 850 ASP Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 2.9990 chunk 339 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 chunk 313 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 756 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32556 Z= 0.188 Angle : 0.665 11.087 44325 Z= 0.328 Chirality : 0.052 0.511 5265 Planarity : 0.004 0.040 5577 Dihedral : 9.213 59.935 6177 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.65 % Allowed : 11.43 % Favored : 85.92 % 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: -0.50 (0.13), residues: 3888 helix: 1.09 (0.21), residues: 651 sheet: 0.96 (0.18), residues: 840 loop : -1.29 (0.11), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 245 HIS 0.004 0.001 HIS B1030 PHE 0.013 0.001 PHE B 483 TYR 0.022 0.001 TYR B 481 ARG 0.003 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 6 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 309 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 219 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 770 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7223 (mtm) REVERT: C 884 MET cc_start: 0.8731 (mmp) cc_final: 0.8358 (mmt) REVERT: C 1045 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 130 PHE cc_start: 0.6337 (m-10) cc_final: 0.6036 (m-10) REVERT: B 144 MET cc_start: 0.7847 (mpp) cc_final: 0.7141 (mpp) REVERT: B 151 MET cc_start: 0.7332 (mmt) cc_final: 0.6902 (mmt) REVERT: B 295 ILE cc_start: 0.8559 (mp) cc_final: 0.8254 (mm) REVERT: B 1045 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8247 (pp) REVERT: G 38 ARG cc_start: 0.7522 (ptt180) cc_final: 0.7199 (ptt-90) REVERT: E 38 ARG cc_start: 0.7438 (ptt180) cc_final: 0.7090 (ptt-90) REVERT: E 50 TYR cc_start: 0.8135 (p90) cc_final: 0.7871 (p90) REVERT: E 64 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.5504 (pttp) REVERT: E 100 LEU cc_start: 0.9138 (tp) cc_final: 0.8929 (tt) REVERT: A 144 MET cc_start: 0.7857 (mpp) cc_final: 0.7462 (mpp) REVERT: A 884 MET cc_start: 0.8751 (mmp) cc_final: 0.8337 (mmt) REVERT: H 64 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5552 (pttp) outliers start: 90 outliers final: 54 residues processed: 284 average time/residue: 0.3966 time to fit residues: 188.6674 Evaluate side-chains 270 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 211 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 849 ASP Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 213 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 77 GLN A 409 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 32556 Z= 0.321 Angle : 0.727 10.164 44325 Z= 0.362 Chirality : 0.054 0.515 5265 Planarity : 0.005 0.038 5577 Dihedral : 9.149 59.963 6177 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.21 % Allowed : 11.84 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.74 (0.13), residues: 3888 helix: 0.89 (0.21), residues: 657 sheet: 0.78 (0.18), residues: 843 loop : -1.46 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 245 HIS 0.005 0.001 HIS C1046 PHE 0.018 0.002 PHE A 89 TYR 0.026 0.002 TYR B 481 ARG 0.005 0.000 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 7 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 327 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 218 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 770 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7278 (mtm) REVERT: C 1045 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 130 PHE cc_start: 0.6612 (m-10) cc_final: 0.6323 (m-10) REVERT: B 144 MET cc_start: 0.7878 (mpp) cc_final: 0.7093 (mpp) REVERT: B 151 MET cc_start: 0.7454 (mmt) cc_final: 0.7139 (mmt) REVERT: B 295 ILE cc_start: 0.8723 (mp) cc_final: 0.8452 (mm) REVERT: B 1045 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (pp) REVERT: G 64 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5590 (pttp) REVERT: G 77 GLN cc_start: 0.8298 (mt0) cc_final: 0.7998 (mt0) REVERT: E 38 ARG cc_start: 0.7497 (ptt180) cc_final: 0.7166 (ptt-90) REVERT: E 50 TYR cc_start: 0.8132 (p90) cc_final: 0.7923 (p90) REVERT: E 64 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.5422 (pttp) REVERT: E 100 LEU cc_start: 0.9213 (tp) cc_final: 0.8968 (tt) REVERT: A 144 MET cc_start: 0.7940 (mpp) cc_final: 0.7595 (mpp) REVERT: H 64 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5510 (pttp) outliers start: 109 outliers final: 86 residues processed: 295 average time/residue: 0.3934 time to fit residues: 193.3187 Evaluate side-chains 302 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 210 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 556 SER Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.9990 chunk 150 optimal weight: 0.0370 chunk 224 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 295 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 32556 Z= 0.162 Angle : 0.631 9.603 44325 Z= 0.308 Chirality : 0.050 0.498 5265 Planarity : 0.004 0.041 5577 Dihedral : 8.547 59.820 6177 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 13.34 % Favored : 84.75 % 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: -0.44 (0.13), residues: 3888 helix: 1.19 (0.21), residues: 660 sheet: 0.82 (0.18), residues: 885 loop : -1.24 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 245 HIS 0.004 0.001 HIS C1030 PHE 0.031 0.001 PHE B 22 TYR 0.026 0.001 TYR B 481 ARG 0.005 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 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 295 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 230 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 PHE cc_start: 0.6102 (m-10) cc_final: 0.5834 (m-10) REVERT: C 484 TYR cc_start: 0.5305 (m-80) cc_final: 0.5103 (m-80) REVERT: C 770 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7109 (mtm) REVERT: C 1045 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 130 PHE cc_start: 0.6498 (m-10) cc_final: 0.6212 (m-10) REVERT: B 144 MET cc_start: 0.7837 (mpp) cc_final: 0.7146 (mpp) REVERT: B 151 MET cc_start: 0.7214 (mmt) cc_final: 0.6999 (mmt) REVERT: B 295 ILE cc_start: 0.8564 (mp) cc_final: 0.8294 (mm) REVERT: B 1045 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8188 (pp) REVERT: G 38 ARG cc_start: 0.7474 (ptt180) cc_final: 0.7164 (ptt-90) REVERT: G 64 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5741 (pttp) REVERT: G 77 GLN cc_start: 0.8222 (mt0) cc_final: 0.7964 (mt0) REVERT: E 38 ARG cc_start: 0.7402 (ptt180) cc_final: 0.7088 (ptt-90) REVERT: A 151 MET cc_start: 0.7343 (mmt) cc_final: 0.6935 (mmt) REVERT: H 50 TYR cc_start: 0.7914 (p90) cc_final: 0.7574 (p90) REVERT: H 64 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5527 (pttp) REVERT: L 18 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.6044 (ptm160) outliers start: 65 outliers final: 45 residues processed: 278 average time/residue: 0.4196 time to fit residues: 194.0762 Evaluate side-chains 275 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 882 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 2.9990 chunk 360 optimal weight: 0.7980 chunk 328 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 152 optimal weight: 0.0010 chunk 275 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 316 optimal weight: 0.7980 chunk 331 optimal weight: 0.5980 chunk 349 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32556 Z= 0.161 Angle : 0.622 9.673 44325 Z= 0.302 Chirality : 0.050 0.491 5265 Planarity : 0.004 0.040 5577 Dihedral : 8.351 59.750 6177 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.94 % Allowed : 13.43 % Favored : 84.63 % 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: -0.38 (0.13), residues: 3888 helix: 1.31 (0.21), residues: 663 sheet: 0.74 (0.17), residues: 927 loop : -1.20 (0.12), residues: 2298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 94 HIS 0.004 0.001 HIS B1030 PHE 0.012 0.001 PHE A 130 TYR 0.028 0.001 TYR B 481 ARG 0.004 0.000 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 9 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 296 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 PHE cc_start: 0.6101 (m-10) cc_final: 0.5842 (m-10) REVERT: C 770 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7102 (mtm) REVERT: C 1045 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 18 ARG cc_start: 0.6642 (OUTLIER) cc_final: 0.4808 (mtm-85) REVERT: B 130 PHE cc_start: 0.6320 (m-10) cc_final: 0.6074 (m-10) REVERT: B 144 MET cc_start: 0.7852 (mpp) cc_final: 0.7154 (mpp) REVERT: B 295 ILE cc_start: 0.8636 (mp) cc_final: 0.8348 (mm) REVERT: B 1045 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8169 (pp) REVERT: G 64 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.5809 (pttp) REVERT: G 77 GLN cc_start: 0.8230 (mt0) cc_final: 0.7999 (mt0) REVERT: E 38 ARG cc_start: 0.7432 (ptt180) cc_final: 0.7093 (ptt-90) REVERT: E 64 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.5426 (pttp) REVERT: A 18 ARG cc_start: 0.7925 (mpp-170) cc_final: 0.7603 (mpp-170) REVERT: A 151 MET cc_start: 0.7352 (mmt) cc_final: 0.6953 (mmt) REVERT: H 64 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5475 (pttp) REVERT: L 105 GLU cc_start: 0.5194 (tp30) cc_final: 0.4937 (tp30) outliers start: 66 outliers final: 48 residues processed: 278 average time/residue: 0.4084 time to fit residues: 187.6691 Evaluate side-chains 275 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 220 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 388 optimal weight: 1.9990 chunk 357 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 238 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32556 Z= 0.223 Angle : 0.658 11.693 44325 Z= 0.322 Chirality : 0.051 0.489 5265 Planarity : 0.004 0.038 5577 Dihedral : 8.387 59.085 6177 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.97 % Allowed : 13.63 % Favored : 84.39 % 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: -0.46 (0.13), residues: 3888 helix: 1.24 (0.21), residues: 663 sheet: 0.73 (0.17), residues: 909 loop : -1.27 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 245 HIS 0.004 0.001 HIS A1030 PHE 0.016 0.001 PHE A 364 TYR 0.031 0.001 TYR B 481 ARG 0.003 0.000 ARG A1021 ********************** REFINEMENT MACRO_CYCLE 10 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 287 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 220 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 770 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7055 (mtm) REVERT: C 1045 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8469 (pp) REVERT: B 18 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.4599 (mtm-85) REVERT: B 130 PHE cc_start: 0.6416 (m-10) cc_final: 0.6164 (m-10) REVERT: B 144 MET cc_start: 0.7865 (mpp) cc_final: 0.7223 (mpp) REVERT: B 295 ILE cc_start: 0.8607 (mp) cc_final: 0.8331 (mm) REVERT: B 1045 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8290 (pp) REVERT: G 64 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.5854 (pttp) REVERT: G 77 GLN cc_start: 0.8268 (mt0) cc_final: 0.8030 (mt0) REVERT: E 38 ARG cc_start: 0.7475 (ptt180) cc_final: 0.7143 (ptt-90) REVERT: A 143 PRO cc_start: 0.7252 (Cg_exo) cc_final: 0.6950 (Cg_endo) REVERT: A 144 MET cc_start: 0.7897 (mpp) cc_final: 0.7627 (mpp) REVERT: H 64 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5608 (pttp) REVERT: L 105 GLU cc_start: 0.5149 (tp30) cc_final: 0.4855 (tp30) outliers start: 67 outliers final: 56 residues processed: 270 average time/residue: 0.4207 time to fit residues: 187.3194 Evaluate side-chains 279 residues out of total 3396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 217 time to evaluate : 3.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 357 ASN Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 71.333 > 50: distance: 59 - 149: 13.786 distance: 62 - 146: 23.148 distance: 74 - 136: 21.138 distance: 109 - 111: 29.763 distance: 112 - 113: 25.541 distance: 112 - 115: 38.573 distance: 113 - 114: 36.215 distance: 113 - 118: 30.034 distance: 115 - 116: 16.498 distance: 115 - 117: 38.893 distance: 118 - 119: 17.117 distance: 119 - 120: 16.419 distance: 119 - 122: 34.599 distance: 120 - 121: 14.558 distance: 120 - 126: 39.032 distance: 122 - 123: 6.340 distance: 122 - 124: 43.562 distance: 123 - 125: 30.231 distance: 126 - 127: 33.742 distance: 127 - 128: 27.116 distance: 128 - 129: 15.572 distance: 128 - 133: 26.584 distance: 130 - 131: 40.486 distance: 133 - 134: 18.387 distance: 134 - 135: 10.757 distance: 134 - 137: 5.248 distance: 135 - 136: 10.860 distance: 135 - 141: 18.084 distance: 137 - 138: 20.327 distance: 138 - 139: 27.220 distance: 138 - 140: 7.206 distance: 141 - 142: 12.680 distance: 142 - 143: 9.135 distance: 142 - 145: 7.407 distance: 143 - 144: 39.845 distance: 143 - 146: 11.429 distance: 146 - 147: 10.520 distance: 147 - 148: 21.433 distance: 147 - 150: 32.348 distance: 148 - 149: 19.433 distance: 148 - 153: 19.343 distance: 150 - 151: 20.968 distance: 150 - 152: 21.585 distance: 153 - 154: 13.411 distance: 154 - 155: 37.323 distance: 154 - 157: 15.434 distance: 155 - 156: 19.875 distance: 155 - 161: 14.186 distance: 157 - 158: 4.846 distance: 158 - 160: 6.770 distance: 161 - 162: 10.905 distance: 162 - 165: 6.171 distance: 163 - 164: 4.231 distance: 165 - 166: 19.610 distance: 166 - 205: 23.836 distance: 167 - 168: 8.120 distance: 168 - 169: 10.049 distance: 169 - 170: 18.214 distance: 169 - 173: 15.352 distance: 171 - 172: 25.684 distance: 173 - 174: 14.151 distance: 174 - 175: 30.428 distance: 174 - 177: 7.652 distance: 175 - 176: 7.659 distance: 175 - 182: 11.688 distance: 177 - 178: 14.764 distance: 178 - 179: 18.905 distance: 179 - 180: 25.510 distance: 179 - 181: 5.994