Starting phenix.real_space_refine on Fri Feb 23 02:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cws_30486/02_2024/7cws_30486.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 162 5.16 5 C 23111 2.51 5 N 5965 2.21 5 O 7151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 20": "NH1" <-> "NH2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 68": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "I TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 68": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "O PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 158": "NH1" <-> "NH2" Residue "O TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 190": "NH1" <-> "NH2" Residue "O TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 214": "NH1" <-> "NH2" Residue "O PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 319": "NH1" <-> "NH2" Residue "O PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1019": "NH1" <-> "NH2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 158": "NH1" <-> "NH2" Residue "Q TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 190": "NH1" <-> "NH2" Residue "Q TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 214": "NH1" <-> "NH2" Residue "Q PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 1019": "NH1" <-> "NH2" Residue "Q PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 158": "NH1" <-> "NH2" Residue "R TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 1019": "NH1" <-> "NH2" Residue "R PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36389 Number of models: 1 Model: "" Number of chains: 33 Chain: "L" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "K" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 8414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8414 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8411 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 51, 'TRANS': 1023} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8411 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 18.75, per 1000 atoms: 0.52 Number of scatterers: 36389 At special positions: 0 Unit cell: (209.04, 216.32, 192.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 162 16.00 O 7151 8.00 N 5965 7.00 C 23111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 136 " distance=2.03 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 166 " distance=2.02 Simple disulfide: pdb=" SG CYS O 291 " - pdb=" SG CYS O 301 " distance=2.03 Simple disulfide: pdb=" SG CYS O 336 " - pdb=" SG CYS O 361 " distance=2.06 Simple disulfide: pdb=" SG CYS O 379 " - pdb=" SG CYS O 432 " distance=2.03 Simple disulfide: pdb=" SG CYS O 480 " - pdb=" SG CYS O 488 " distance=2.03 Simple disulfide: pdb=" SG CYS O 617 " - pdb=" SG CYS O 649 " distance=2.02 Simple disulfide: pdb=" SG CYS O 662 " - pdb=" SG CYS O 671 " distance=2.03 Simple disulfide: pdb=" SG CYS O 738 " - pdb=" SG CYS O 760 " distance=2.03 Simple disulfide: pdb=" SG CYS O 743 " - pdb=" SG CYS O 749 " distance=2.03 Simple disulfide: pdb=" SG CYS O1032 " - pdb=" SG CYS O1043 " distance=2.00 Simple disulfide: pdb=" SG CYS O1082 " - pdb=" SG CYS O1126 " distance=2.00 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 136 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 166 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 291 " - pdb=" SG CYS Q 301 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 336 " - pdb=" SG CYS Q 361 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 379 " - pdb=" SG CYS Q 432 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 480 " - pdb=" SG CYS Q 488 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 617 " - pdb=" SG CYS Q 649 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 662 " - pdb=" SG CYS Q 671 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 738 " - pdb=" SG CYS Q 760 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 743 " - pdb=" SG CYS Q 749 " distance=2.02 Simple disulfide: pdb=" SG CYS Q1032 " - pdb=" SG CYS Q1043 " distance=2.04 Simple disulfide: pdb=" SG CYS Q1082 " - pdb=" SG CYS Q1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 136 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 166 " distance=2.02 Simple disulfide: pdb=" SG CYS R 291 " - pdb=" SG CYS R 301 " distance=2.09 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.04 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS R 617 " - pdb=" SG CYS R 649 " distance=2.03 Simple disulfide: pdb=" SG CYS R 662 " - pdb=" SG CYS R 671 " distance=2.03 Simple disulfide: pdb=" SG CYS R 738 " - pdb=" SG CYS R 760 " distance=2.02 Simple disulfide: pdb=" SG CYS R 743 " - pdb=" SG CYS R 749 " distance=2.02 Simple disulfide: pdb=" SG CYS R1032 " - pdb=" SG CYS R1043 " distance=2.04 Simple disulfide: pdb=" SG CYS R1082 " - pdb=" SG CYS R1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG J 1 " - " NAG J 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 1 " - " ASN O 234 " " NAG B 1 " - " ASN O 717 " " NAG J 1 " - " ASN O 801 " " NAG O1201 " - " ASN O 603 " " NAG O1202 " - " ASN O 616 " " NAG O1203 " - " ASN O 657 " " NAG O1204 " - " ASN O 709 " " NAG O1205 " - " ASN O1074 " " NAG Q1301 " - " ASN Q 61 " " NAG Q1302 " - " ASN Q 603 " " NAG Q1303 " - " ASN Q 616 " " NAG Q1304 " - " ASN Q 657 " " NAG Q1305 " - " ASN Q 709 " " NAG Q1306 " - " ASN Q1074 " " NAG R1201 " - " ASN R 603 " " NAG R1202 " - " ASN R 616 " " NAG R1203 " - " ASN R 657 " " NAG R1204 " - " ASN R 709 " " NAG R1205 " - " ASN R1074 " " NAG S 1 " - " ASN O1098 " " NAG T 1 " - " ASN O1134 " " NAG U 1 " - " ASN Q 234 " " NAG V 1 " - " ASN Q 717 " " NAG W 1 " - " ASN Q 801 " " NAG X 1 " - " ASN Q1098 " " NAG Y 1 " - " ASN Q1134 " " NAG a 1 " - " ASN R 717 " " NAG b 1 " - " ASN R 801 " " NAG c 1 " - " ASN R1134 " " NAG d 1 " - " ASN R1098 " Time building additional restraints: 15.46 Conformation dependent library (CDL) restraints added in 6.7 seconds 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8544 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 89 sheets defined 16.4% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'K' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU K 84 " --> pdb=" O THR K 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'O' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 343 Processing helix chain 'O' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG O 408 " --> pdb=" O ASP O 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 405 through 408' Processing helix chain 'O' and resid 416 through 421 Processing helix chain 'O' and resid 737 through 743 Processing helix chain 'O' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU O 752 " --> pdb=" O GLU O 748 " (cutoff:3.500A) Processing helix chain 'O' and resid 755 through 757 No H-bonds generated for 'chain 'O' and resid 755 through 757' Processing helix chain 'O' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU O 763 " --> pdb=" O PHE O 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN O 764 " --> pdb=" O CYS O 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU O 773 " --> pdb=" O GLY O 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP O 775 " --> pdb=" O ALA O 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 776 " --> pdb=" O VAL O 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR O 778 " --> pdb=" O GLN O 774 " (cutoff:3.500A) Processing helix chain 'O' and resid 816 through 826 removed outlier: 3.635A pdb=" N LEU O 821 " --> pdb=" O PHE O 817 " (cutoff:3.500A) Processing helix chain 'O' and resid 849 through 856 Processing helix chain 'O' and resid 866 through 885 removed outlier: 3.705A pdb=" N LEU O 878 " --> pdb=" O THR O 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR O 883 " --> pdb=" O ALA O 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY O 885 " --> pdb=" O THR O 881 " (cutoff:3.500A) Processing helix chain 'O' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA O 903 " --> pdb=" O ALA O 899 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN O 907 " --> pdb=" O ALA O 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE O 909 " --> pdb=" O ARG O 905 " (cutoff:3.500A) Processing helix chain 'O' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR O 917 " --> pdb=" O GLN O 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU O 918 " --> pdb=" O ASN O 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS O 921 " --> pdb=" O TYR O 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU O 922 " --> pdb=" O GLU O 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE O 934 " --> pdb=" O ALA O 930 " (cutoff:3.500A) Processing helix chain 'O' and resid 945 through 965 Processing helix chain 'O' and resid 966 through 968 No H-bonds generated for 'chain 'O' and resid 966 through 968' Processing helix chain 'O' and resid 976 through 982 removed outlier: 3.540A pdb=" N ILE O 980 " --> pdb=" O VAL O 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 981 " --> pdb=" O LEU O 977 " (cutoff:3.500A) Processing helix chain 'O' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA O 989 " --> pdb=" O ASP O 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL O 991 " --> pdb=" O VAL O 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP O 994 " --> pdb=" O GLU O 990 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG O 995 " --> pdb=" O VAL O 991 " (cutoff:3.500A) Processing helix chain 'O' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU O1144 " --> pdb=" O PRO O1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP O1146 " --> pdb=" O GLN O1142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 343 Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.681A pdb=" N VAL Q 367 " --> pdb=" O ASP Q 364 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR Q 369 " --> pdb=" O SER Q 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 408 removed outlier: 3.555A pdb=" N ARG Q 408 " --> pdb=" O ASP Q 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 405 through 408' Processing helix chain 'Q' and resid 416 through 421 Processing helix chain 'Q' and resid 737 through 743 Processing helix chain 'Q' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU Q 752 " --> pdb=" O GLU Q 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU Q 754 " --> pdb=" O SER Q 750 " (cutoff:3.500A) Processing helix chain 'Q' and resid 755 through 757 No H-bonds generated for 'chain 'Q' and resid 755 through 757' Processing helix chain 'Q' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN Q 764 " --> pdb=" O CYS Q 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP Q 775 " --> pdb=" O ALA Q 771 " (cutoff:3.500A) Processing helix chain 'Q' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP Q 820 " --> pdb=" O SER Q 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Q 821 " --> pdb=" O PHE Q 817 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN Q 856 " --> pdb=" O ALA Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU Q 878 " --> pdb=" O THR Q 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY Q 885 " --> pdb=" O THR Q 881 " (cutoff:3.500A) Processing helix chain 'Q' and resid 886 through 890 Processing helix chain 'Q' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA Q 903 " --> pdb=" O ALA Q 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR Q 904 " --> pdb=" O MET Q 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE Q 909 " --> pdb=" O ARG Q 905 " (cutoff:3.500A) Processing helix chain 'Q' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU Q 918 " --> pdb=" O ASN Q 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS Q 921 " --> pdb=" O TYR Q 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU Q 922 " --> pdb=" O GLU Q 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS Q 933 " --> pdb=" O SER Q 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN Q 935 " --> pdb=" O ILE Q 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP Q 936 " --> pdb=" O GLY Q 932 " (cutoff:3.500A) Processing helix chain 'Q' and resid 945 through 965 Processing helix chain 'Q' and resid 966 through 968 No H-bonds generated for 'chain 'Q' and resid 966 through 968' Processing helix chain 'Q' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE Q 980 " --> pdb=" O VAL Q 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU Q 981 " --> pdb=" O LEU Q 977 " (cutoff:3.500A) Processing helix chain 'Q' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL Q 991 " --> pdb=" O VAL Q 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Q 995 " --> pdb=" O VAL Q 991 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1116 through 1118 No H-bonds generated for 'chain 'Q' and resid 1116 through 1118' Processing helix chain 'Q' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU Q1144 " --> pdb=" O PRO Q1140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP Q1146 " --> pdb=" O GLN Q1142 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 304 removed outlier: 3.749A pdb=" N THR R 299 " --> pdb=" O PRO R 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.240A pdb=" N GLN R 409 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 737 through 743 Processing helix chain 'R' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU R 752 " --> pdb=" O GLU R 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU R 754 " --> pdb=" O SER R 750 " (cutoff:3.500A) Processing helix chain 'R' and resid 755 through 757 No H-bonds generated for 'chain 'R' and resid 755 through 757' Processing helix chain 'R' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN R 764 " --> pdb=" O CYS R 760 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP R 775 " --> pdb=" O ALA R 771 " (cutoff:3.500A) Processing helix chain 'R' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP R 820 " --> pdb=" O SER R 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU R 821 " --> pdb=" O PHE R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN R 856 " --> pdb=" O ALA R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU R 878 " --> pdb=" O THR R 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY R 885 " --> pdb=" O THR R 881 " (cutoff:3.500A) Processing helix chain 'R' and resid 886 through 890 Processing helix chain 'R' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA R 903 " --> pdb=" O ALA R 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR R 904 " --> pdb=" O MET R 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE R 909 " --> pdb=" O ARG R 905 " (cutoff:3.500A) Processing helix chain 'R' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU R 918 " --> pdb=" O ASN R 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS R 921 " --> pdb=" O TYR R 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU R 922 " --> pdb=" O GLU R 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS R 933 " --> pdb=" O SER R 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN R 935 " --> pdb=" O ILE R 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP R 936 " --> pdb=" O GLY R 932 " (cutoff:3.500A) Processing helix chain 'R' and resid 945 through 965 Processing helix chain 'R' and resid 966 through 968 No H-bonds generated for 'chain 'R' and resid 966 through 968' Processing helix chain 'R' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE R 980 " --> pdb=" O VAL R 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU R 981 " --> pdb=" O LEU R 977 " (cutoff:3.500A) Processing helix chain 'R' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL R 991 " --> pdb=" O VAL R 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 995 " --> pdb=" O VAL R 991 " (cutoff:3.500A) Processing helix chain 'R' and resid 1116 through 1118 No H-bonds generated for 'chain 'R' and resid 1116 through 1118' Processing helix chain 'R' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU R1144 " --> pdb=" O PRO R1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP R1146 " --> pdb=" O GLN R1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN L 3 " --> pdb=" O SER L 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA L 80 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 46 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR C 91 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 100 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.512A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.338A pdb=" N GLN F 10 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.085A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.511A pdb=" N GLN H 10 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.588A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN N 3 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA N 80 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 46 through 49 Processing sheet with id=AC5, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR K 50 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR K 91 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL K 100 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AC8, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP M 86 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR M 91 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL M 100 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 20 through 23 Processing sheet with id=AD5, first strand: chain 'O' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER O 31 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER O 60 " --> pdb=" O SER O 31 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL O 36 " --> pdb=" O LEU O 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA O 222 " --> pdb=" O HIS O 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS O 207 " --> pdb=" O ALA O 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU O 224 " --> pdb=" O SER O 205 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER O 205 " --> pdb=" O GLU O 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE O 203 " --> pdb=" O LEU O 226 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP O 228 " --> pdb=" O PHE O 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE O 201 " --> pdb=" O ASP O 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS O 195 " --> pdb=" O LYS O 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU O 191 " --> pdb=" O LYS O 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA O 263 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR O 51 " --> pdb=" O PHE O 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP O 287 " --> pdb=" O LYS O 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'O' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE O 101 " --> pdb=" O ALA O 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA O 243 " --> pdb=" O ILE O 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY O 103 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 116 through 120 removed outlier: 6.402A pdb=" N GLU O 132 " --> pdb=" O CYS O 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS O 166 " --> pdb=" O GLU O 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN O 134 " --> pdb=" O ASN O 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN O 164 " --> pdb=" O GLN O 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR O 599 " --> pdb=" O GLY O 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL O 595 " --> pdb=" O THR O 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY O 594 " --> pdb=" O GLN O 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE O 326 " --> pdb=" O ASN O 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 357 through 358 removed outlier: 4.021A pdb=" N VAL O 395 " --> pdb=" O ILE O 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 361 through 362 removed outlier: 6.367A pdb=" N CYS O 361 " --> pdb=" O CYS O 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'O' and resid 378 through 379 Processing sheet with id=AE7, first strand: chain 'O' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'O' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'O' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR O 553 " --> pdb=" O ASP O 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 654 through 655 removed outlier: 6.349A pdb=" N GLU O 654 " --> pdb=" O ALA O 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR O 696 " --> pdb=" O GLU O 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER O 673 " --> pdb=" O ILE O 693 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA O 672 " --> pdb=" O PRO O 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 701 through 702 removed outlier: 6.502A pdb=" N ALA O 701 " --> pdb=" O ILE R 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'O' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE O 714 " --> pdb=" O LYS O1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS O1073 " --> pdb=" O ILE O 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE O1095 " --> pdb=" O ALA O1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY O1059 " --> pdb=" O SER O1055 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER O1055 " --> pdb=" O GLY O1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL O1061 " --> pdb=" O PRO O1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU O1063 " --> pdb=" O SER O1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER O1051 " --> pdb=" O LEU O1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL O1065 " --> pdb=" O LEU O1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 735 through 736 Processing sheet with id=AF6, first strand: chain 'O' and resid 787 through 788 Processing sheet with id=AF7, first strand: chain 'O' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'Q' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN Q 61 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR Q 269 " --> pdb=" O ASN Q 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA Q 263 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU Q 191 " --> pdb=" O LYS Q 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS Q 195 " --> pdb=" O LYS Q 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE Q 201 " --> pdb=" O ASP Q 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP Q 228 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE Q 203 " --> pdb=" O LEU Q 226 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER Q 205 " --> pdb=" O GLU Q 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU Q 224 " --> pdb=" O SER Q 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS Q 207 " --> pdb=" O ALA Q 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA Q 222 " --> pdb=" O HIS Q 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Q 36 " --> pdb=" O LEU Q 223 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 28 through 31 Processing sheet with id=AG1, first strand: chain 'Q' and resid 48 through 55 Processing sheet with id=AG2, first strand: chain 'Q' and resid 84 through 85 Processing sheet with id=AG3, first strand: chain 'Q' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE Q 101 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA Q 243 " --> pdb=" O ILE Q 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY Q 103 " --> pdb=" O LEU Q 241 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU Q 132 " --> pdb=" O CYS Q 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS Q 166 " --> pdb=" O GLU Q 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN Q 134 " --> pdb=" O ASN Q 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN Q 164 " --> pdb=" O GLN Q 134 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL Q 595 " --> pdb=" O THR Q 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN Q 317 " --> pdb=" O GLY Q 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY Q 593 " --> pdb=" O ASN Q 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY Q 594 " --> pdb=" O GLN Q 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE Q 326 " --> pdb=" O ASN Q 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR Q 553 " --> pdb=" O ASP Q 586 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL Q 395 " --> pdb=" O ILE Q 358 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS Q 361 " --> pdb=" O CYS Q 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Q' and resid 378 through 379 Processing sheet with id=AH1, first strand: chain 'Q' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'Q' and resid 473 through 474 Processing sheet with id=AH3, first strand: chain 'Q' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU Q 654 " --> pdb=" O ALA Q 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR Q 696 " --> pdb=" O GLU Q 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE Q 670 " --> pdb=" O ILE Q 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 711 through 715 removed outlier: 3.844A pdb=" N ILE Q 714 " --> pdb=" O LYS Q1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA Q1078 " --> pdb=" O PHE Q1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE Q1095 " --> pdb=" O ALA Q1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Q' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY Q1059 " --> pdb=" O SER Q1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER Q1055 " --> pdb=" O GLY Q1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL Q1061 " --> pdb=" O PRO Q1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU Q1063 " --> pdb=" O SER Q1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER Q1051 " --> pdb=" O LEU Q1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL Q1065 " --> pdb=" O LEU Q1049 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 734 through 736 Processing sheet with id=AH7, first strand: chain 'Q' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE Q 788 " --> pdb=" O ASN R 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'Q' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA Q1087 " --> pdb=" O SER Q1123 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA R 27 " --> pdb=" O TRP R 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER R 60 " --> pdb=" O SER R 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN R 61 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR R 269 " --> pdb=" O ASN R 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR R 265 " --> pdb=" O PHE R 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU R 191 " --> pdb=" O LYS R 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 195 " --> pdb=" O LYS R 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE R 201 " --> pdb=" O ASP R 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP R 228 " --> pdb=" O PHE R 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE R 203 " --> pdb=" O LEU R 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER R 205 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU R 224 " --> pdb=" O SER R 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS R 207 " --> pdb=" O ALA R 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA R 222 " --> pdb=" O HIS R 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL R 36 " --> pdb=" O LEU R 223 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 48 through 55 removed outlier: 7.192A pdb=" N THR R 274 " --> pdb=" O ASP R 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP R 290 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU R 276 " --> pdb=" O ALA R 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA R 288 " --> pdb=" O LEU R 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS R 278 " --> pdb=" O THR R 286 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 69 through 70 Processing sheet with id=AI3, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=AI4, first strand: chain 'R' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE R 101 " --> pdb=" O ALA R 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA R 243 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY R 103 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU R 132 " --> pdb=" O CYS R 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS R 166 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN R 134 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN R 164 " --> pdb=" O GLN R 134 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 311 through 319 removed outlier: 3.841A pdb=" N VAL R 595 " --> pdb=" O THR R 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN R 317 " --> pdb=" O GLY R 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY R 593 " --> pdb=" O ASN R 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY R 594 " --> pdb=" O GLN R 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'R' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR R 553 " --> pdb=" O ASP R 586 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI9 Processing sheet with id=AJ1, first strand: chain 'R' and resid 378 through 379 Processing sheet with id=AJ2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AJ3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AJ4, first strand: chain 'R' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU R 654 " --> pdb=" O ALA R 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR R 696 " --> pdb=" O GLU R 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE R 670 " --> pdb=" O ILE R 666 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 711 through 715 removed outlier: 3.848A pdb=" N ILE R 714 " --> pdb=" O LYS R1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR R1076 " --> pdb=" O SER R1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA R1078 " --> pdb=" O PHE R1095 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE R1095 " --> pdb=" O ALA R1078 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY R1059 " --> pdb=" O SER R1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER R1055 " --> pdb=" O GLY R1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL R1061 " --> pdb=" O PRO R1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU R1063 " --> pdb=" O SER R1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER R1051 " --> pdb=" O LEU R1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL R1065 " --> pdb=" O LEU R1049 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 734 through 736 Processing sheet with id=AJ8, first strand: chain 'R' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA R1087 " --> pdb=" O SER R1123 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3066 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.63 Time building geometry restraints manager: 16.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8577 1.33 - 1.45: 9733 1.45 - 1.58: 18697 1.58 - 1.71: 0 1.71 - 1.83: 213 Bond restraints: 37220 Sorted by residual: bond pdb=" N CYS O 336 " pdb=" CA CYS O 336 " ideal model delta sigma weight residual 1.457 1.521 -0.064 1.41e-02 5.03e+03 2.08e+01 bond pdb=" CA SER O 60 " pdb=" CB SER O 60 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" N THR O 588 " pdb=" CA THR O 588 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.80e-03 1.04e+04 1.42e+01 bond pdb=" N LEU O 24 " pdb=" CA LEU O 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.35e+01 bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 37215 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.43: 861 105.43 - 112.72: 19525 112.72 - 120.00: 13404 120.00 - 127.29: 16487 127.29 - 134.57: 352 Bond angle restraints: 50629 Sorted by residual: angle pdb=" N ILE O 100 " pdb=" CA ILE O 100 " pdb=" C ILE O 100 " ideal model delta sigma weight residual 113.20 102.84 10.36 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N ILE R 100 " pdb=" CA ILE R 100 " pdb=" C ILE R 100 " ideal model delta sigma weight residual 113.20 102.87 10.33 9.60e-01 1.09e+00 1.16e+02 angle pdb=" C TYR D 95 " pdb=" CA TYR D 95 " pdb=" CB TYR D 95 " ideal model delta sigma weight residual 110.67 124.25 -13.58 1.52e+00 4.33e-01 7.99e+01 angle pdb=" N CYS Q 301 " pdb=" CA CYS Q 301 " pdb=" C CYS Q 301 " ideal model delta sigma weight residual 113.23 102.37 10.86 1.24e+00 6.50e-01 7.67e+01 angle pdb=" N LYS O 386 " pdb=" CA LYS O 386 " pdb=" C LYS O 386 " ideal model delta sigma weight residual 113.38 103.29 10.09 1.23e+00 6.61e-01 6.73e+01 ... (remaining 50624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 21555 16.86 - 33.71: 866 33.71 - 50.57: 192 50.57 - 67.43: 43 67.43 - 84.28: 27 Dihedral angle restraints: 22683 sinusoidal: 9348 harmonic: 13335 Sorted by residual: dihedral pdb=" CB CYS Q1082 " pdb=" SG CYS Q1082 " pdb=" SG CYS Q1126 " pdb=" CB CYS Q1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.99 72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS R1082 " pdb=" SG CYS R1082 " pdb=" SG CYS R1126 " pdb=" CB CYS R1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.92 72.92 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS O1082 " pdb=" SG CYS O1082 " pdb=" SG CYS O1126 " pdb=" CB CYS O1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.28 72.28 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 22680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5810 0.315 - 0.631: 17 0.631 - 0.946: 0 0.946 - 1.261: 0 1.261 - 1.577: 2 Chirality restraints: 5829 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN O 234 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN Q 234 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.10e+01 ... (remaining 5826 not shown) Planarity restraints: 6491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG d 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.88e+02 pdb=" C7 NAG d 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG d 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG d 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG d 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " 0.262 2.00e-02 2.50e+03 2.23e-01 6.24e+02 pdb=" C7 NAG T 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN O 234 " 0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN O 234 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN O 234 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN O 234 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 6488 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 28 2.15 - 2.84: 12432 2.84 - 3.52: 52267 3.52 - 4.21: 89359 4.21 - 4.90: 149155 Nonbonded interactions: 303241 Sorted by model distance: nonbonded pdb=" CD2 LEU R 48 " pdb=" CE2 PHE R 306 " model vdw 1.462 3.760 nonbonded pdb=" OD1 ASP L 110 " pdb=" CD PRO L 111 " model vdw 1.753 3.440 nonbonded pdb=" CD1 LEU Q 48 " pdb=" O LYS Q 304 " model vdw 1.804 3.460 nonbonded pdb=" OE2 GLU Q 324 " pdb=" CG2 VAL Q 534 " model vdw 1.847 3.460 nonbonded pdb=" CG2 THR O 63 " pdb=" CZ PHE O 65 " model vdw 1.853 3.760 ... (remaining 303236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'J' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = (chain 'O' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 345 or (resid 346 and (name N or n \ ame CA or name C or name O or name CB )) or resid 347 through 1147 or resid 1201 \ through 1205)) selection = (chain 'Q' and (resid 14 through 345 or (resid 346 and (name N or name CA or nam \ e C or name O or name CB )) or resid 347 through 698 or (resid 699 and (name N o \ r name CA or name C or name O or name CB )) or resid 700 through 1147 or resid 1 \ 301 through 1305)) selection = (chain 'R' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 698 or (resid 699 and (name N or n \ ame CA or name C or name O or name CB )) or resid 700 through 1147 or resid 1201 \ through 1205)) } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.810 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 98.990 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5394 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 : 0.008 0.069 37220 Z= 0.552 Angle : 1.129 13.771 50629 Z= 0.713 Chirality : 0.074 1.577 5829 Planarity : 0.008 0.281 6461 Dihedral : 10.377 84.285 13995 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 32.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.83 % Favored : 92.98 % Rotamer: Outliers : 0.20 % Allowed : 1.99 % Favored : 97.81 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.39 (0.10), residues: 4542 helix: -3.27 (0.14), residues: 642 sheet: -1.84 (0.13), residues: 1089 loop : -2.23 (0.10), residues: 2811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP O 353 HIS 0.012 0.002 HIS G 35 PHE 0.046 0.003 PHE Q 347 TYR 0.034 0.003 TYR G 50 ARG 0.012 0.001 ARG R 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 372 time to evaluate : 4.154 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: O 973 ILE cc_start: 0.7617 (pt) cc_final: 0.7166 (pt) REVERT: R 1139 ASP cc_start: 0.5357 (t0) cc_final: 0.5037 (t0) outliers start: 8 outliers final: 1 residues processed: 380 average time/residue: 0.5209 time to fit residues: 316.9713 Evaluate side-chains 153 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 4.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 3.9990 chunk 343 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 355 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 215 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 411 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN L 66 GLN C 6 GLN C 53 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 36 GLN F 37 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 91 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 66 GLN K 6 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN P 66 GLN M 6 GLN O 61 ASN O 146 HIS O 148 ASN O 271 GLN O 282 ASN O 317 ASN O 437 ASN O 655 HIS ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 913 GLN ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1010 GLN O1119 ASN Q 121 ASN Q 122 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 317 ASN Q 437 ASN ** Q 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 606 ASN Q 655 HIS ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 913 GLN ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1010 GLN R 121 ASN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 271 GLN ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN R 655 HIS ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 913 GLN ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1010 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 37220 Z= 0.288 Angle : 0.750 13.331 50629 Z= 0.394 Chirality : 0.049 0.714 5829 Planarity : 0.005 0.054 6461 Dihedral : 7.802 56.805 5897 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.18 % Favored : 95.64 % Rotamer: Outliers : 1.21 % Allowed : 6.54 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.11), residues: 4542 helix: -1.15 (0.18), residues: 657 sheet: -1.40 (0.14), residues: 1200 loop : -1.75 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 112 HIS 0.009 0.002 HIS L 36 PHE 0.031 0.002 PHE N 109 TYR 0.030 0.002 TYR G 50 ARG 0.010 0.001 ARG O 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 3.927 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: H 103 LEU cc_start: 0.1329 (tp) cc_final: 0.0582 (mp) outliers start: 48 outliers final: 19 residues processed: 217 average time/residue: 0.5001 time to fit residues: 179.3476 Evaluate side-chains 142 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain P residue 71 MET Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain Q residue 69 HIS Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 556 ASN Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1089 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 0.7980 chunk 127 optimal weight: 0.0470 chunk 342 optimal weight: 0.9990 chunk 280 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 412 optimal weight: 0.8980 chunk 445 optimal weight: 0.9990 chunk 367 optimal weight: 0.8980 chunk 408 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 330 optimal weight: 6.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 564 GLN ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 901 GLN ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 957 GLN ** O1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1119 ASN Q 121 ASN Q 271 GLN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 913 GLN ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 957 GLN ** Q1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 ASN R 540 ASN ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37220 Z= 0.175 Angle : 0.625 13.553 50629 Z= 0.324 Chirality : 0.046 0.657 5829 Planarity : 0.004 0.063 6461 Dihedral : 6.653 58.247 5896 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.60 % Favored : 95.20 % Rotamer: Outliers : 1.38 % Allowed : 8.22 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4542 helix: 0.13 (0.20), residues: 663 sheet: -1.22 (0.15), residues: 1107 loop : -1.38 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 112 HIS 0.005 0.001 HIS G 35 PHE 0.021 0.002 PHE N 109 TYR 0.020 0.002 TYR G 50 ARG 0.008 0.000 ARG R 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 4.325 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: H 103 LEU cc_start: 0.1514 (tp) cc_final: 0.0626 (mp) REVERT: O 287 ASP cc_start: 0.7264 (m-30) cc_final: 0.6992 (m-30) outliers start: 55 outliers final: 22 residues processed: 199 average time/residue: 0.4804 time to fit residues: 160.2052 Evaluate side-chains 144 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 373 SER Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 556 ASN Chi-restraints excluded: chain R residue 620 VAL Chi-restraints excluded: chain R residue 675 GLN Chi-restraints excluded: chain R residue 869 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 196 optimal weight: 2.9990 chunk 276 optimal weight: 30.0000 chunk 413 optimal weight: 5.9990 chunk 437 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 391 optimal weight: 50.0000 chunk 118 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Q 121 ASN ** Q 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37220 Z= 0.202 Angle : 0.594 15.253 50629 Z= 0.304 Chirality : 0.045 0.597 5829 Planarity : 0.004 0.072 6461 Dihedral : 6.069 57.421 5896 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.32 % Favored : 95.49 % Rotamer: Outliers : 1.81 % Allowed : 8.17 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4542 helix: 0.53 (0.20), residues: 672 sheet: -1.00 (0.15), residues: 1092 loop : -1.34 (0.12), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 112 HIS 0.005 0.001 HIS I 35 PHE 0.019 0.001 PHE N 109 TYR 0.018 0.001 TYR G 50 ARG 0.008 0.000 ARG N 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 142 time to evaluate : 3.913 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: L 60 MET cc_start: 0.4214 (ptm) cc_final: 0.3353 (tmm) REVERT: L 82 MET cc_start: 0.4511 (ttt) cc_final: 0.4101 (ptm) REVERT: D 46 LEU cc_start: 0.0420 (OUTLIER) cc_final: 0.0129 (mt) REVERT: H 103 LEU cc_start: 0.1857 (tp) cc_final: 0.0858 (mp) REVERT: N 82 MET cc_start: 0.5000 (ttm) cc_final: 0.4472 (ptm) REVERT: O 287 ASP cc_start: 0.7331 (m-30) cc_final: 0.6934 (m-30) REVERT: O 906 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: Q 906 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: R 902 MET cc_start: 0.7698 (mmm) cc_final: 0.7465 (mmt) REVERT: R 906 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7747 (m-80) outliers start: 72 outliers final: 36 residues processed: 204 average time/residue: 0.4989 time to fit residues: 172.9199 Evaluate side-chains 158 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 437 ASN Chi-restraints excluded: chain O residue 620 VAL Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain Q residue 30 ASN Chi-restraints excluded: chain Q residue 73 THR Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 437 ASN Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 286 THR Chi-restraints excluded: chain R residue 437 ASN Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 675 GLN Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1089 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 326 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 373 optimal weight: 4.9990 chunk 302 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 223 optimal weight: 6.9990 chunk 393 optimal weight: 40.0000 chunk 110 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 53 ASN O 115 GLN O 501 ASN ** O 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 914 ASN ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Q 69 HIS ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 414 GLN Q 501 ASN Q 540 ASN Q 606 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 ASN R 501 ASN R 762 GLN ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 37220 Z= 0.520 Angle : 0.797 19.449 50629 Z= 0.412 Chirality : 0.051 0.522 5829 Planarity : 0.005 0.072 6461 Dihedral : 6.659 58.372 5896 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.27 % Favored : 93.53 % Rotamer: Outliers : 2.34 % Allowed : 8.55 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4542 helix: 0.11 (0.20), residues: 636 sheet: -1.14 (0.15), residues: 1062 loop : -1.62 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 112 HIS 0.027 0.003 HIS E 35 PHE 0.041 0.003 PHE Q1062 TYR 0.030 0.003 TYR O 789 ARG 0.007 0.001 ARG R1091 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 139 time to evaluate : 3.728 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: E 73 ASP cc_start: 0.3056 (t0) cc_final: 0.1355 (m-30) REVERT: N 33 VAL cc_start: 0.2170 (OUTLIER) cc_final: 0.1826 (m) REVERT: N 82 MET cc_start: 0.5296 (ttm) cc_final: 0.4553 (ptm) REVERT: O 1144 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.6091 (mt-10) REVERT: Q 1089 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: R 128 ILE cc_start: 0.6555 (mm) cc_final: 0.6313 (mm) REVERT: R 906 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7997 (m-80) outliers start: 93 outliers final: 56 residues processed: 217 average time/residue: 0.4482 time to fit residues: 166.5054 Evaluate side-chains 168 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 4.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 87 ASN Chi-restraints excluded: chain O residue 501 ASN Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1081 ILE Chi-restraints excluded: chain O residue 1089 PHE Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain O residue 1144 GLU Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 282 ASN Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 377 PHE Chi-restraints excluded: chain Q residue 437 ASN Chi-restraints excluded: chain Q residue 501 ASN Chi-restraints excluded: chain Q residue 556 ASN Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 7.9990 chunk 394 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 438 optimal weight: 0.9990 chunk 363 optimal weight: 0.0170 chunk 202 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 762 GLN ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 955 ASN Q 121 ASN Q 501 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 37220 Z= 0.259 Angle : 0.629 15.467 50629 Z= 0.322 Chirality : 0.045 0.506 5829 Planarity : 0.004 0.072 6461 Dihedral : 6.089 58.516 5896 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.37 % Favored : 94.43 % Rotamer: Outliers : 1.86 % Allowed : 9.55 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4542 helix: 0.48 (0.20), residues: 648 sheet: -1.10 (0.15), residues: 1101 loop : -1.58 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 112 HIS 0.007 0.001 HIS Q1048 PHE 0.016 0.002 PHE L 65 TYR 0.020 0.002 TYR E 50 ARG 0.006 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 115 time to evaluate : 3.903 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: E 73 ASP cc_start: 0.3160 (t0) cc_final: 0.1612 (m-30) REVERT: F 36 GLN cc_start: 0.5041 (OUTLIER) cc_final: 0.4189 (pm20) REVERT: N 82 MET cc_start: 0.5240 (ttm) cc_final: 0.4472 (ptm) REVERT: O 906 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: Q 501 ASN cc_start: -0.0658 (OUTLIER) cc_final: -0.1049 (m-40) REVERT: Q 906 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: Q 1089 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7626 (m-10) REVERT: R 906 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7841 (m-80) outliers start: 74 outliers final: 48 residues processed: 179 average time/residue: 0.4716 time to fit residues: 145.1997 Evaluate side-chains 160 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 599 THR Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1089 PHE Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 315 THR Chi-restraints excluded: chain Q residue 501 ASN Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 869 MET Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 675 GLN Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1081 ILE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 249 optimal weight: 30.0000 chunk 320 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 368 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 273 optimal weight: 30.0000 chunk 266 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 613 GLN ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 ASN ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37220 Z= 0.275 Angle : 0.615 14.109 50629 Z= 0.314 Chirality : 0.045 0.496 5829 Planarity : 0.004 0.067 6461 Dihedral : 5.873 58.790 5896 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.79 % Favored : 94.03 % Rotamer: Outliers : 2.04 % Allowed : 9.93 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4542 helix: 0.65 (0.20), residues: 660 sheet: -0.88 (0.16), residues: 1038 loop : -1.59 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 112 HIS 0.006 0.001 HIS Q1048 PHE 0.016 0.002 PHE R 823 TYR 0.020 0.002 TYR Q 508 ARG 0.018 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 111 time to evaluate : 3.785 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: L 60 MET cc_start: 0.4454 (ptm) cc_final: 0.4094 (tmm) REVERT: L 82 MET cc_start: 0.4228 (ttm) cc_final: 0.3994 (ptm) REVERT: E 73 ASP cc_start: 0.3296 (t0) cc_final: 0.1779 (m-30) REVERT: E 107 MET cc_start: -0.0102 (mmm) cc_final: -0.0499 (mtt) REVERT: F 36 GLN cc_start: 0.5060 (OUTLIER) cc_final: 0.4225 (pm20) REVERT: N 82 MET cc_start: 0.5150 (ttm) cc_final: 0.4392 (ptm) REVERT: O 906 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: Q 906 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: Q 1089 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: R 906 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7843 (m-80) outliers start: 81 outliers final: 58 residues processed: 180 average time/residue: 0.4475 time to fit residues: 139.9375 Evaluate side-chains 167 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 104 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 599 THR Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 976 VAL Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1089 PHE Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 282 ASN Chi-restraints excluded: chain Q residue 289 VAL Chi-restraints excluded: chain Q residue 312 ILE Chi-restraints excluded: chain Q residue 315 THR Chi-restraints excluded: chain Q residue 377 PHE Chi-restraints excluded: chain Q residue 611 LEU Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 794 ILE Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain Q residue 976 VAL Chi-restraints excluded: chain Q residue 1089 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 976 VAL Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1081 ILE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1114 ILE Chi-restraints excluded: chain R residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 8.9990 chunk 174 optimal weight: 0.0270 chunk 260 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 277 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 40 optimal weight: 30.0000 chunk 343 optimal weight: 0.2980 overall best weight: 1.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 37220 Z= 0.177 Angle : 0.575 12.345 50629 Z= 0.292 Chirality : 0.044 0.483 5829 Planarity : 0.004 0.065 6461 Dihedral : 5.489 57.853 5896 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 1.51 % Allowed : 10.48 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4542 helix: 0.97 (0.20), residues: 660 sheet: -0.65 (0.16), residues: 1032 loop : -1.51 (0.11), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 112 HIS 0.005 0.001 HIS Q1048 PHE 0.020 0.001 PHE O1095 TYR 0.022 0.001 TYR M 50 ARG 0.004 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 3.940 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: L 60 MET cc_start: 0.4603 (ptm) cc_final: 0.4102 (tmm) REVERT: L 82 MET cc_start: 0.3878 (ttm) cc_final: 0.3569 (ptm) REVERT: E 73 ASP cc_start: 0.3235 (t0) cc_final: 0.1819 (m-30) REVERT: F 36 GLN cc_start: 0.4974 (OUTLIER) cc_final: 0.4427 (pm20) REVERT: N 82 MET cc_start: 0.4962 (ttm) cc_final: 0.4280 (ptm) REVERT: O 906 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: Q 906 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: R 906 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7712 (m-80) outliers start: 60 outliers final: 41 residues processed: 160 average time/residue: 0.4598 time to fit residues: 127.7817 Evaluate side-chains 148 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 PHE Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 118 LEU Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 312 ILE Chi-restraints excluded: chain Q residue 752 LEU Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 675 GLN Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1081 ILE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 0.6980 chunk 418 optimal weight: 0.8980 chunk 381 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 0.6980 chunk 319 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 367 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 405 optimal weight: 0.5980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 501 ASN ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN Q 501 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 ASN R 282 ASN ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 37220 Z= 0.204 Angle : 0.577 12.674 50629 Z= 0.291 Chirality : 0.044 0.475 5829 Planarity : 0.004 0.062 6461 Dihedral : 5.324 58.231 5896 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.46 % Favored : 94.41 % Rotamer: Outliers : 1.56 % Allowed : 10.53 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4542 helix: 1.18 (0.21), residues: 651 sheet: -0.58 (0.16), residues: 1017 loop : -1.47 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 112 HIS 0.007 0.001 HIS G 35 PHE 0.019 0.001 PHE O 133 TYR 0.021 0.001 TYR M 50 ARG 0.004 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 111 time to evaluate : 4.168 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: L 60 MET cc_start: 0.4552 (ptm) cc_final: 0.4080 (tmm) REVERT: E 73 ASP cc_start: 0.3419 (t0) cc_final: 0.1969 (m-30) REVERT: F 36 GLN cc_start: 0.5004 (OUTLIER) cc_final: 0.4443 (pm20) REVERT: G 3 GLN cc_start: 0.2963 (tp-100) cc_final: 0.2733 (tp40) REVERT: N 82 MET cc_start: 0.4908 (ttm) cc_final: 0.4208 (ptm) REVERT: O 906 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: Q 501 ASN cc_start: -0.0493 (OUTLIER) cc_final: -0.0893 (m-40) REVERT: Q 906 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: R 906 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7765 (m-80) outliers start: 62 outliers final: 45 residues processed: 165 average time/residue: 0.4664 time to fit residues: 132.3728 Evaluate side-chains 155 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 87 ARG Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 200 TYR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 599 THR Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 773 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1094 VAL Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 282 ASN Chi-restraints excluded: chain Q residue 312 ILE Chi-restraints excluded: chain Q residue 315 THR Chi-restraints excluded: chain Q residue 501 ASN Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Chi-restraints excluded: chain R residue 1081 ILE Chi-restraints excluded: chain R residue 1089 PHE Chi-restraints excluded: chain R residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.1980 chunk 430 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 299 optimal weight: 4.9990 chunk 451 optimal weight: 4.9990 chunk 415 optimal weight: 0.9980 chunk 359 optimal weight: 0.3980 chunk 37 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 37220 Z= 0.151 Angle : 0.552 11.678 50629 Z= 0.278 Chirality : 0.044 0.471 5829 Planarity : 0.004 0.057 6461 Dihedral : 5.080 57.738 5896 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 1.18 % Allowed : 10.68 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4542 helix: 1.29 (0.21), residues: 660 sheet: -0.39 (0.16), residues: 1020 loop : -1.41 (0.11), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 112 HIS 0.006 0.001 HIS E 35 PHE 0.013 0.001 PHE Q 643 TYR 0.021 0.001 TYR M 50 ARG 0.004 0.000 ARG R 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9084 Ramachandran restraints generated. 4542 Oldfield, 0 Emsley, 4542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 3.854 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: L 60 MET cc_start: 0.4535 (ptm) cc_final: 0.4261 (tmm) REVERT: E 73 ASP cc_start: 0.3200 (t0) cc_final: 0.1800 (m-30) REVERT: F 36 GLN cc_start: 0.5303 (OUTLIER) cc_final: 0.4759 (pm20) REVERT: G 3 GLN cc_start: 0.2946 (tp-100) cc_final: 0.2738 (tp40) REVERT: N 82 MET cc_start: 0.4708 (ttm) cc_final: 0.4086 (ptm) REVERT: O 906 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: Q 906 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: R 906 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7646 (m-80) outliers start: 47 outliers final: 38 residues processed: 156 average time/residue: 0.4568 time to fit residues: 121.2818 Evaluate side-chains 143 residues out of total 3987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 69 HIS Chi-restraints excluded: chain O residue 200 TYR Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 556 ASN Chi-restraints excluded: chain O residue 661 GLU Chi-restraints excluded: chain O residue 794 ILE Chi-restraints excluded: chain O residue 816 SER Chi-restraints excluded: chain O residue 906 PHE Chi-restraints excluded: chain O residue 973 ILE Chi-restraints excluded: chain O residue 1032 CYS Chi-restraints excluded: chain O residue 1104 VAL Chi-restraints excluded: chain O residue 1130 ILE Chi-restraints excluded: chain O residue 1136 THR Chi-restraints excluded: chain Q residue 213 VAL Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 315 THR Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 906 PHE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 534 VAL Chi-restraints excluded: chain R residue 546 LEU Chi-restraints excluded: chain R residue 740 MET Chi-restraints excluded: chain R residue 794 ILE Chi-restraints excluded: chain R residue 869 MET Chi-restraints excluded: chain R residue 906 PHE Chi-restraints excluded: chain R residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 40.0000 chunk 382 optimal weight: 5.9990 chunk 110 optimal weight: 50.0000 chunk 331 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 359 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 369 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 GLN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 501 ASN ** Q 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.116818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.087801 restraints weight = 155980.376| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 4.04 r_work: 0.3497 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 37220 Z= 0.434 Angle : 0.690 14.836 50629 Z= 0.353 Chirality : 0.048 0.465 5829 Planarity : 0.004 0.055 6461 Dihedral : 5.715 58.795 5896 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.69 % Favored : 93.17 % Rotamer: Outliers : 1.36 % Allowed : 10.68 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4542 helix: 0.71 (0.20), residues: 654 sheet: -0.70 (0.16), residues: 1044 loop : -1.51 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 37 HIS 0.010 0.002 HIS O1088 PHE 0.028 0.002 PHE R 823 TYR 0.021 0.002 TYR O1138 ARG 0.006 0.001 ARG R 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6662.22 seconds wall clock time: 123 minutes 40.83 seconds (7420.83 seconds total)