Starting phenix.real_space_refine on Fri Apr 5 20:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyb_27073/04_2024/8cyb_27073_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 121 5.16 5 C 17866 2.51 5 N 4555 2.21 5 O 5687 1.98 5 H 25897 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 54126 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 16912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16912 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 16923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16923 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 16900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 16900 Classifications: {'peptide': 1102} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1913 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 70 Unusual residues: {'BMA': 1, 'FUC': 2, 'GAL': 1, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" 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: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 165 Unusual residues: {'AH2': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.71, per 1000 atoms: 0.33 Number of scatterers: 54126 At special positions: 0 Unit cell: (164.796, 159.48, 195.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 O 5687 8.00 N 4555 7.00 C 17866 6.00 H 25897 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS D 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA J 3 " - " MAN J 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA V 3 " - " MAN V 5 " BETA1-2 " GAL I 3 " - " FUC I 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA1-3 " NAG N 1 " - " FUC N 4 " " NAG X 1 " - " FUC X 2 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 5 " " FUC I 2 " - " GAL I 3 " " NAG I 5 " - " BMA I 6 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " NAG I 1 " - " FUC I 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 149 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 234 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 657 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 17 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 234 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 603 " " NAG C1310 " - " ASN C 657 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 709 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 616 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 33.62 Conformation dependent library (CDL) restraints added in 4.1 seconds 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 45 sheets defined 20.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.548A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.795A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 850 through 853 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 914 through 940 removed outlier: 7.045A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.052A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.189A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.048A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 617 through 623 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.728A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 4.243A pdb=" N GLN B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 921 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.110A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.321A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 339 through 342 No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 617 through 619 No H-bonds generated for 'chain 'C' and resid 617 through 619' Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.952A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.520A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 914 through 939 removed outlier: 3.696A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 967 removed outlier: 3.955A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.346A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.872A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.889A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.929A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 168 through 171 removed outlier: 6.545A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id= E, first strand: chain 'A' and resid 354 through 358 Processing sheet with id= F, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= G, first strand: chain 'A' and resid 575 through 577 Processing sheet with id= H, first strand: chain 'A' and resid 642 through 645 removed outlier: 4.000A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.431A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 712 through 715 Processing sheet with id= K, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.601A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= M, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= N, first strand: chain 'A' and resid 140 through 146 removed outlier: 5.775A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.126A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.694A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.922A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 354 through 358 Processing sheet with id= T, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= U, first strand: chain 'B' and resid 538 through 543 Processing sheet with id= V, first strand: chain 'B' and resid 642 through 645 removed outlier: 4.629A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 693 through 696 removed outlier: 6.230A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= Y, first strand: chain 'B' and resid 719 through 728 removed outlier: 5.564A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 734 through 736 Processing sheet with id= AA, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AB, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id= AC, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.746A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.928A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 168 through 171 removed outlier: 6.356A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 354 through 358 Processing sheet with id= AG, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AH, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.811A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AJ, first strand: chain 'C' and resid 642 through 645 removed outlier: 4.706A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 693 through 696 removed outlier: 6.527A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AM, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.550A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AO, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= AP, first strand: chain 'C' and resid 142 through 144 removed outlier: 5.747A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 19 through 23 Processing sheet with id= AR, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.322A pdb=" N THR D 138 " --> pdb=" O VAL D 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'D' and resid 135 through 137 removed outlier: 5.591A pdb=" N ARG D 54 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N PHE D 63 " --> pdb=" O ARG D 54 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.62 Time building geometry restraints manager: 35.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 25888 1.03 - 1.23: 95 1.23 - 1.42: 12197 1.42 - 1.62: 16423 1.62 - 1.82: 153 Bond restraints: 54756 Sorted by residual: bond pdb=" C1 MAN M 4 " pdb=" C2 MAN M 4 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 MAN M 4 " pdb=" O5 MAN M 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.592 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C1 BMA Z 3 " pdb=" C2 BMA Z 3 " ideal model delta sigma weight residual 1.519 1.579 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C1 BMA I 6 " pdb=" C2 BMA I 6 " ideal model delta sigma weight residual 1.519 1.578 -0.059 2.00e-02 2.50e+03 8.65e+00 ... (remaining 54751 not shown) Histogram of bond angle deviations from ideal: 72.31 - 84.64: 19 84.64 - 96.98: 0 96.98 - 109.32: 32921 109.32 - 121.65: 54513 121.65 - 133.99: 10438 Bond angle restraints: 97891 Sorted by residual: angle pdb=" C ASP A 253 " pdb=" CA ASP A 253 " pdb=" HA ASP A 253 " ideal model delta sigma weight residual 109.00 72.31 36.69 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C ASP B 253 " pdb=" CA ASP B 253 " pdb=" HA ASP B 253 " ideal model delta sigma weight residual 109.00 72.32 36.68 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C ASP C 253 " pdb=" CA ASP C 253 " pdb=" HA ASP C 253 " ideal model delta sigma weight residual 109.00 72.69 36.31 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C ALA B 292 " pdb=" CA ALA B 292 " pdb=" HA ALA B 292 " ideal model delta sigma weight residual 109.00 73.28 35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ALA A 292 " pdb=" CA ALA A 292 " pdb=" HA ALA A 292 " ideal model delta sigma weight residual 109.00 73.93 35.07 3.00e+00 1.11e-01 1.37e+02 ... (remaining 97886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 26145 24.21 - 48.42: 1161 48.42 - 72.63: 333 72.63 - 96.84: 164 96.84 - 121.05: 114 Dihedral angle restraints: 27917 sinusoidal: 15922 harmonic: 11995 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 155.59 -62.59 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual 180.00 148.20 31.80 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.19 -38.19 1 1.00e+01 1.00e-02 2.05e+01 ... (remaining 27914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4217 0.079 - 0.157: 533 0.157 - 0.236: 8 0.236 - 0.314: 17 0.314 - 0.393: 5 Chirality restraints: 4780 Sorted by residual: chirality pdb=" CA ALA A 292 " pdb=" N ALA A 292 " pdb=" C ALA A 292 " pdb=" CB ALA A 292 " both_signs ideal model delta sigma weight residual False 2.48 2.09 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ASP C 253 " pdb=" N ASP C 253 " pdb=" C ASP C 253 " pdb=" CB ASP C 253 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 4777 not shown) Planarity restraints: 8233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO B 39 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 84 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 85 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 630 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 631 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 631 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 631 " -0.028 5.00e-02 4.00e+02 ... (remaining 8230 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2471 2.18 - 2.79: 105982 2.79 - 3.39: 145585 3.39 - 4.00: 194241 4.00 - 4.60: 296533 Nonbonded interactions: 744812 Sorted by model distance: nonbonded pdb=" HE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 1.575 1.850 nonbonded pdb=" O VAL C 36 " pdb=" H LEU C 223 " model vdw 1.585 1.850 nonbonded pdb=" O ASN C 334 " pdb=" H VAL C 362 " model vdw 1.597 1.850 nonbonded pdb=" H ALA A 292 " pdb=" HA ALA A 292 " model vdw 1.599 1.816 nonbonded pdb=" O VAL B 327 " pdb="HD22 ASN B 532 " model vdw 1.601 1.850 ... (remaining 744807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name H \ D1 or name HD2 or name HE1 or name HE2)) or resid 201 through 230 or (resid 231 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name H \ G22 or name HG23 or name HD11 or name HD12 or name HD13)) or resid 232 through 3 \ 56 or (resid 357 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12 or name HH21)) or resid 358 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ or name H or name HA )) or resid 530 or (resid \ 531 and (name N or name CA or name C or name O or name H or name HA )) or resid \ 532 through 562 or (resid 563 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name \ HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 564 through 11 \ 47 or resid 1301 through 1310)) selection = (chain 'B' and (resid 13 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3)) or resid 42 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 170 th \ rough 230 or (resid 231 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG1 \ 3 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13) \ ) or resid 232 through 290 or (resid 291 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 292 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 302 thr \ ough 320 or (resid 321 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 322 through 527 or (resid 528 through 529 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE o \ r name NZ or name H or name HA )) or resid 530 or (resid 531 and (name N or name \ CA or name C or name O or name H or name HA )) or resid 532 through 1147 or res \ id 1301 through 1310)) selection = (chain 'C' and (resid 13 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3)) or resid 42 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 170 th \ rough 199 or (resid 200 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH o \ r name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 \ or name HE2)) or resid 201 through 290 or (resid 291 and (name N or name CA or n \ ame C or name O or name CB or name SG or name H or name HA or name HB2 or name H \ B3)) or resid 292 through 300 or (resid 301 and (name N or name CA or name C or \ name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or r \ esid 302 through 320 or (resid 321 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 322 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or name H \ H12 or name HH21)) or resid 358 through 537 or (resid 538 and (name N or name CA \ or name C or name O or name CB or name SG or name H or name HA or name HB2 or n \ ame HB3)) or resid 539 through 562 or (resid 563 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 564 through 589 or (resid 590 and (name N or name CA or name C or name O or \ name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 591 \ through 1063 or (resid 1064 and (name N or name CA or name C or name O or name C \ B or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 1065 th \ rough 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'V' } ncs_group { reference = (chain 'L' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) } ncs_group { reference = (chain 'N' and resid 1 through 3) selection = (chain 'W' and resid 1 through 3) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.590 Extract box with map and model: 8.700 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 135.550 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.360 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:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28859 Z= 0.235 Angle : 0.616 7.616 39296 Z= 0.272 Chirality : 0.049 0.393 4780 Planarity : 0.003 0.066 4926 Dihedral : 19.332 121.046 12071 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.04 % Favored : 94.70 % Rotamer: Outliers : 0.20 % Allowed : 0.37 % Favored : 99.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3412 helix: 2.50 (0.22), residues: 674 sheet: 0.29 (0.18), residues: 751 loop : -1.21 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 152 HIS 0.002 0.000 HIS C 207 PHE 0.012 0.001 PHE C 541 TYR 0.010 0.001 TYR C 265 ARG 0.001 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 3.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8460 (tp-100) outliers start: 6 outliers final: 7 residues processed: 178 average time/residue: 1.7929 time to fit residues: 395.6468 Evaluate side-chains 124 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.9980 chunk 259 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 0.0000 chunk 268 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 199 optimal weight: 0.4980 chunk 310 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28859 Z= 0.162 Angle : 0.535 8.917 39296 Z= 0.248 Chirality : 0.047 0.395 4780 Planarity : 0.003 0.064 4926 Dihedral : 15.146 119.441 6021 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.16 % Favored : 94.58 % Rotamer: Outliers : 0.40 % Allowed : 3.76 % Favored : 95.83 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3412 helix: 2.64 (0.21), residues: 665 sheet: 0.25 (0.18), residues: 755 loop : -1.23 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.002 0.000 HIS C1064 PHE 0.020 0.001 PHE C 318 TYR 0.011 0.001 TYR C1067 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8472 (tp-100) outliers start: 12 outliers final: 10 residues processed: 134 average time/residue: 1.9276 time to fit residues: 319.3985 Evaluate side-chains 124 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 311 optimal weight: 0.9990 chunk 336 optimal weight: 9.9990 chunk 277 optimal weight: 0.0170 chunk 308 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28859 Z= 0.192 Angle : 0.505 8.810 39296 Z= 0.242 Chirality : 0.046 0.395 4780 Planarity : 0.003 0.050 4926 Dihedral : 12.198 122.262 6019 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.16 % Favored : 94.55 % Rotamer: Outliers : 0.57 % Allowed : 4.50 % Favored : 94.93 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3412 helix: 2.58 (0.21), residues: 666 sheet: 0.28 (0.18), residues: 769 loop : -1.28 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 52 HIS 0.004 0.000 HIS C1064 PHE 0.013 0.001 PHE C 392 TYR 0.013 0.001 TYR C1067 ARG 0.003 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8482 (tp-100) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 1.7922 time to fit residues: 307.6443 Evaluate side-chains 120 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1075 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 148 optimal weight: 50.0000 chunk 208 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28859 Z= 0.406 Angle : 0.593 12.309 39296 Z= 0.296 Chirality : 0.047 0.408 4780 Planarity : 0.004 0.052 4926 Dihedral : 10.929 120.976 6019 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.55 % Rotamer: Outliers : 0.74 % Allowed : 5.78 % Favored : 93.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3412 helix: 1.85 (0.21), residues: 671 sheet: 0.07 (0.18), residues: 801 loop : -1.49 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.009 0.001 HIS C1064 PHE 0.020 0.001 PHE C 201 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8474 (tp-100) REVERT: D 50 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.1616 (tpt) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 1.6646 time to fit residues: 245.8385 Evaluate side-chains 109 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 4.9990 chunk 187 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 296 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28859 Z= 0.176 Angle : 0.503 8.545 39296 Z= 0.249 Chirality : 0.046 0.391 4780 Planarity : 0.003 0.051 4926 Dihedral : 10.295 119.769 6017 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Rotamer: Outliers : 0.64 % Allowed : 6.62 % Favored : 92.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3412 helix: 2.12 (0.21), residues: 668 sheet: 0.16 (0.18), residues: 789 loop : -1.38 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 64 HIS 0.023 0.001 HIS A 66 PHE 0.013 0.001 PHE C 541 TYR 0.012 0.001 TYR C1067 ARG 0.006 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8492 (tp-100) REVERT: A 869 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8839 (mtt) REVERT: C 177 MET cc_start: 0.4068 (mpt) cc_final: 0.2860 (pmm) REVERT: D 50 MET cc_start: 0.3642 (OUTLIER) cc_final: 0.1516 (tpt) outliers start: 19 outliers final: 12 residues processed: 112 average time/residue: 1.7877 time to fit residues: 252.0123 Evaluate side-chains 108 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 330 optimal weight: 40.0000 chunk 274 optimal weight: 5.9990 chunk 153 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28859 Z= 0.231 Angle : 0.506 8.073 39296 Z= 0.251 Chirality : 0.045 0.410 4780 Planarity : 0.003 0.050 4926 Dihedral : 9.784 119.829 6017 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.72 % Favored : 93.96 % Rotamer: Outliers : 0.64 % Allowed : 6.82 % Favored : 92.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3412 helix: 2.14 (0.21), residues: 668 sheet: 0.11 (0.18), residues: 803 loop : -1.38 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 52 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE C 855 TYR 0.013 0.001 TYR C1067 ARG 0.002 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8495 (tp-100) REVERT: B 661 GLU cc_start: 0.7976 (pp20) cc_final: 0.7640 (pp20) REVERT: D 50 MET cc_start: 0.3408 (OUTLIER) cc_final: 0.1138 (tpt) outliers start: 19 outliers final: 14 residues processed: 116 average time/residue: 1.8270 time to fit residues: 266.1668 Evaluate side-chains 109 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 187 optimal weight: 0.4980 chunk 278 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 329 optimal weight: 0.0870 chunk 206 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28859 Z= 0.178 Angle : 0.493 8.009 39296 Z= 0.244 Chirality : 0.045 0.441 4780 Planarity : 0.003 0.050 4926 Dihedral : 9.371 119.614 6017 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.19 % Favored : 94.49 % Rotamer: Outliers : 0.60 % Allowed : 6.89 % Favored : 92.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3412 helix: 2.22 (0.21), residues: 668 sheet: 0.15 (0.18), residues: 795 loop : -1.35 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 52 HIS 0.003 0.000 HIS C1064 PHE 0.013 0.001 PHE C 541 TYR 0.012 0.001 TYR C1067 ARG 0.001 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8478 (tp-100) REVERT: B 661 GLU cc_start: 0.7954 (pp20) cc_final: 0.7621 (pp20) REVERT: C 855 PHE cc_start: 0.7596 (m-80) cc_final: 0.7353 (m-10) REVERT: D 50 MET cc_start: 0.3213 (OUTLIER) cc_final: 0.0824 (tpt) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 1.7022 time to fit residues: 240.9930 Evaluate side-chains 111 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 360 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28859 Z= 0.310 Angle : 0.529 6.653 39296 Z= 0.264 Chirality : 0.046 0.463 4780 Planarity : 0.004 0.051 4926 Dihedral : 9.145 119.790 6017 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 0.67 % Allowed : 6.96 % Favored : 92.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3412 helix: 2.00 (0.21), residues: 673 sheet: 0.09 (0.18), residues: 804 loop : -1.46 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS C1064 PHE 0.015 0.001 PHE A 201 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8504 (tp-100) REVERT: B 661 GLU cc_start: 0.8012 (pp20) cc_final: 0.7682 (pp20) REVERT: D 50 MET cc_start: 0.3217 (OUTLIER) cc_final: 0.0772 (tpt) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 1.8457 time to fit residues: 257.1949 Evaluate side-chains 107 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 307 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 241 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 277 optimal weight: 4.9990 chunk 290 optimal weight: 0.9990 chunk 306 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28859 Z= 0.161 Angle : 0.496 7.942 39296 Z= 0.246 Chirality : 0.046 0.467 4780 Planarity : 0.003 0.047 4926 Dihedral : 8.770 119.391 6013 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.98 % Favored : 94.70 % Rotamer: Outliers : 0.60 % Allowed : 7.26 % Favored : 92.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3412 helix: 2.15 (0.21), residues: 674 sheet: 0.13 (0.18), residues: 796 loop : -1.37 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 52 HIS 0.003 0.000 HIS A 66 PHE 0.029 0.001 PHE C 855 TYR 0.014 0.001 TYR C 200 ARG 0.002 0.000 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8475 (tp-100) REVERT: B 200 TYR cc_start: 0.8459 (m-80) cc_final: 0.8020 (t80) REVERT: D 50 MET cc_start: 0.3571 (OUTLIER) cc_final: 0.0630 (tpt) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 1.8804 time to fit residues: 264.2108 Evaluate side-chains 109 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 154 optimal weight: 30.0000 chunk 225 optimal weight: 5.9990 chunk 340 optimal weight: 40.0000 chunk 313 optimal weight: 1.9990 chunk 271 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28859 Z= 0.250 Angle : 0.516 8.374 39296 Z= 0.257 Chirality : 0.046 0.459 4780 Planarity : 0.003 0.049 4926 Dihedral : 8.522 119.246 6013 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.01 % Favored : 93.67 % Rotamer: Outliers : 0.50 % Allowed : 7.69 % Favored : 91.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.47 (0.14), residues: 3412 helix: 2.08 (0.21), residues: 674 sheet: 0.09 (0.18), residues: 792 loop : -1.43 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 PHE 0.017 0.001 PHE A 592 TYR 0.015 0.001 TYR C1067 ARG 0.002 0.000 ARG C1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6824 Ramachandran restraints generated. 3412 Oldfield, 0 Emsley, 3412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue TYR 200 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Residue LYS 278 is missing expected H atoms. Skipping. Residue LEU 335 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue LYS 528 is missing expected H atoms. Skipping. Residue LYS 529 is missing expected H atoms. Skipping. Residue THR 531 is missing expected H atoms. Skipping. Residue LEU 699 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8489 (tp-100) REVERT: A 1144 GLU cc_start: 0.9022 (tp30) cc_final: 0.8600 (tp30) REVERT: B 200 TYR cc_start: 0.8462 (m-80) cc_final: 0.8028 (t80) REVERT: D 50 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.0797 (tpt) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 1.6846 time to fit residues: 229.4190 Evaluate side-chains 107 residues out of total 2990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 50 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.146891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083704 restraints weight = 174479.146| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.27 r_work: 0.3071 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28859 Z= 0.212 Angle : 0.504 9.207 39296 Z= 0.252 Chirality : 0.045 0.424 4780 Planarity : 0.003 0.048 4926 Dihedral : 8.345 119.030 6013 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.28 % Favored : 94.43 % Rotamer: Outliers : 0.47 % Allowed : 7.80 % Favored : 91.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.45 (0.14), residues: 3412 helix: 2.11 (0.21), residues: 674 sheet: 0.10 (0.18), residues: 788 loop : -1.41 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.000 HIS A 66 PHE 0.030 0.001 PHE C 855 TYR 0.014 0.001 TYR C 200 ARG 0.002 0.000 ARG C1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10598.92 seconds wall clock time: 184 minutes 16.65 seconds (11056.65 seconds total)