Starting phenix.real_space_refine on Fri Feb 23 01:36:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cwu_30488/02_2024/7cwu_30488.pdb" } resolution = 3.5 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 22886 2.51 5 N 5998 2.21 5 O 7082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 55": "NH1" <-> "NH2" 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 "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 68": "NH1" <-> "NH2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "O ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36128 Number of models: 1 Model: "" Number of chains: 33 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: "I" 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: "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: "G" 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: "J" 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: "F" 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: "B" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8392 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8340 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 50, 'TRANS': 1018} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 8387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8387 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 1023} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "B" 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: "C" 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: "A" 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: 36128 At special positions: 0 Unit cell: (202.8, 216.32, 208, 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 7082 8.00 N 5998 7.00 C 22886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.09 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 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 A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN C 234 " " NAG Q 1 " - " ASN A 801 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN A 717 " Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 6.6 seconds 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8500 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 18.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU G 84 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.139A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.909A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.953A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.981A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.635A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.705A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.540A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.141A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.953A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.642A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.749A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.643A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'O' and resid 74 through 76 No H-bonds generated for 'chain 'O' and resid 74 through 76' Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, 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=AA2, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AA4, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP I 86 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR I 91 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL I 100 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 20 through 23 Processing sheet with id=AA7, 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=AA8, 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=AA9, first strand: chain 'N' and resid 46 through 49 Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR G 91 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL G 100 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 23 Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN J 3 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA J 80 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 49 Processing sheet with id=AB7, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR F 91 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL F 100 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 23 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.402A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.349A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.502A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.844A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.192A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AG4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AG5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AH1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.848A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AH7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AH9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR M 113 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 4 through 7 removed outlier: 11.871A pdb=" N CYS R 23 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR R 74 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ALA R 25 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR R 72 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN R 27 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP R 70 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AI8, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR O 113 " --> pdb=" O TYR O 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'S' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS S 23 " --> pdb=" O THR S 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR S 74 " --> pdb=" O CYS S 23 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ALA S 25 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR S 72 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN S 27 " --> pdb=" O ASP S 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP S 70 " --> pdb=" O GLN S 27 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU S 105 " --> pdb=" O LEU S 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3108 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: 17.09 Time building geometry restraints manager: 15.79 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: 8578 1.33 - 1.45: 9288 1.45 - 1.58: 18848 1.58 - 1.70: 0 1.70 - 1.83: 213 Bond restraints: 36927 Sorted by residual: bond pdb=" CA SER B 60 " pdb=" CB SER B 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 B 588 " pdb=" CA THR B 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 B 24 " pdb=" CA LEU B 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 K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 36922 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.41: 819 105.41 - 112.66: 19358 112.66 - 119.92: 12734 119.92 - 127.18: 16951 127.18 - 134.44: 355 Bond angle restraints: 50217 Sorted by residual: angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 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 A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 113.20 102.87 10.33 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS C 301 " pdb=" CA CYS C 301 " pdb=" C CYS C 301 " ideal model delta sigma weight residual 113.23 102.37 10.86 1.24e+00 6.50e-01 7.67e+01 angle pdb=" CA GLY A 283 " pdb=" C GLY A 283 " pdb=" O GLY A 283 " ideal model delta sigma weight residual 122.56 116.28 6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" C ASP N 110 " pdb=" CA ASP N 110 " pdb=" CB ASP N 110 " ideal model delta sigma weight residual 110.17 121.42 -11.25 1.97e+00 2.58e-01 3.26e+01 ... (remaining 50212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 21466 16.86 - 33.71: 794 33.71 - 50.57: 205 50.57 - 67.43: 42 67.43 - 84.28: 21 Dihedral angle restraints: 22528 sinusoidal: 9256 harmonic: 13272 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " 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 A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " 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 B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.28 72.28 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 22525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5783 0.315 - 0.631: 11 0.631 - 0.946: 0 0.946 - 1.261: 0 1.261 - 1.577: 2 Chirality restraints: 5796 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 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 E 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 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 T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 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 5793 not shown) Planarity restraints: 6449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.88e+02 pdb=" C7 NAG T 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " 0.262 2.00e-02 2.50e+03 2.23e-01 6.24e+02 pdb=" C7 NAG Y 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN B 234 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 6446 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 7 1.85 - 2.61: 617 2.61 - 3.38: 48580 3.38 - 4.14: 88172 4.14 - 4.90: 156749 Nonbonded interactions: 294125 Sorted by model distance: nonbonded pdb=" O PRO B 527 " pdb=" CG LYS B 529 " model vdw 1.089 3.440 nonbonded pdb=" CD2 LEU A 48 " pdb=" CE2 PHE A 306 " model vdw 1.462 3.760 nonbonded pdb=" CB PRO B 527 " pdb=" CD LYS B 529 " model vdw 1.635 3.840 nonbonded pdb=" O PRO A 527 " pdb=" CG LYS A 529 " model vdw 1.741 3.440 nonbonded pdb=" OD1 ASP P 110 " pdb=" CD PRO P 111 " model vdw 1.753 3.440 ... (remaining 294120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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 328 or resid 334 through 527 or re \ sid 531 through 698 or (resid 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 1147 or resid 1301 through 1305)) selection = (chain 'B' 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 328 or resid 334 through 527 or re \ sid 531 through 1147 or resid 1301 through 1305)) selection = (chain 'C' and (resid 14 through 698 or (resid 699 and (name N or name CA or nam \ e C or name O or name CB )) or resid 700 through 1147 or resid 1301 through 1305 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'Q' 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 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.040 Extract box with map and model: 7.600 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 97.480 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5460 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 36927 Z= 0.523 Angle : 1.052 11.253 50217 Z= 0.645 Chirality : 0.069 1.577 5796 Planarity : 0.008 0.281 6419 Dihedral : 10.179 84.285 13875 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 0.25 % Allowed : 1.58 % Favored : 98.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.61 (0.10), residues: 4526 helix: -3.25 (0.15), residues: 598 sheet: -2.11 (0.14), residues: 1047 loop : -2.41 (0.09), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 47 HIS 0.011 0.002 HIS B1048 PHE 0.035 0.003 PHE C 392 TYR 0.030 0.003 TYR M 94 ARG 0.014 0.001 ARG S 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 379 time to evaluate : 4.114 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: B 51 THR cc_start: 0.7795 (p) cc_final: 0.7185 (p) REVERT: B 287 ASP cc_start: 0.6680 (t0) cc_final: 0.6128 (m-30) REVERT: C 52 GLN cc_start: 0.7811 (pt0) cc_final: 0.7457 (pp30) REVERT: A 66 HIS cc_start: 0.4870 (m-70) cc_final: 0.4423 (m-70) outliers start: 10 outliers final: 3 residues processed: 389 average time/residue: 0.5358 time to fit residues: 328.4875 Evaluate side-chains 165 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 0.8980 chunk 343 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 355 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 215 optimal weight: 0.2980 chunk 264 optimal weight: 0.9980 chunk 411 optimal weight: 50.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN I 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN F 6 GLN B 61 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 317 ASN B 498 GLN B 501 ASN B 556 ASN B 655 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1119 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 501 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 234 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN H 39 GLN H 84 ASN H 104 ASN L 38 GLN L 55 GLN M 39 GLN M 84 ASN M 104 ASN R 38 GLN R 55 GLN O 39 GLN O 84 ASN O 104 ASN S 38 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 36927 Z= 0.193 Angle : 0.680 11.072 50217 Z= 0.352 Chirality : 0.047 0.732 5796 Planarity : 0.004 0.052 6419 Dihedral : 7.641 58.713 5899 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 1.30 % Allowed : 5.75 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.58 (0.11), residues: 4526 helix: -0.99 (0.18), residues: 653 sheet: -1.51 (0.14), residues: 1085 loop : -2.04 (0.10), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 64 HIS 0.007 0.001 HIS B 66 PHE 0.028 0.002 PHE A 106 TYR 0.028 0.002 TYR B 421 ARG 0.009 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 217 time to evaluate : 3.636 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: B 52 GLN cc_start: 0.8656 (pm20) cc_final: 0.7993 (pp30) REVERT: B 237 ARG cc_start: 0.6608 (ptm-80) cc_final: 0.6279 (ptm-80) REVERT: B 287 ASP cc_start: 0.6928 (t0) cc_final: 0.6698 (m-30) REVERT: B 531 THR cc_start: 0.7044 (p) cc_final: 0.6794 (m) REVERT: C 64 TRP cc_start: 0.7718 (t60) cc_final: 0.7288 (t60) REVERT: A 52 GLN cc_start: 0.8618 (pm20) cc_final: 0.7881 (pp30) REVERT: A 64 TRP cc_start: 0.7863 (t60) cc_final: 0.7618 (t60) REVERT: H 103 MET cc_start: 0.3423 (OUTLIER) cc_final: 0.2472 (tpp) REVERT: O 121 SER cc_start: 0.3880 (t) cc_final: 0.3531 (p) outliers start: 51 outliers final: 24 residues processed: 252 average time/residue: 0.4840 time to fit residues: 201.8390 Evaluate side-chains 166 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 342 optimal weight: 0.9980 chunk 280 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 412 optimal weight: 30.0000 chunk 445 optimal weight: 0.9990 chunk 367 optimal weight: 0.0980 chunk 408 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 chunk 330 optimal weight: 30.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 87 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN A 188 ASN A 271 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN M 39 GLN O 39 GLN S 55 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 36927 Z= 0.198 Angle : 0.622 13.962 50217 Z= 0.318 Chirality : 0.046 0.611 5796 Planarity : 0.004 0.062 6419 Dihedral : 6.482 58.928 5898 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 1.48 % Allowed : 7.66 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.90 (0.12), residues: 4526 helix: 0.30 (0.20), residues: 667 sheet: -1.13 (0.14), residues: 1205 loop : -1.79 (0.11), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 152 HIS 0.008 0.001 HIS B 66 PHE 0.028 0.002 PHE B 86 TYR 0.025 0.001 TYR B 421 ARG 0.007 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 163 time to evaluate : 3.840 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: B 52 GLN cc_start: 0.8735 (pm20) cc_final: 0.7895 (pp30) REVERT: B 237 ARG cc_start: 0.6636 (ptm-80) cc_final: 0.6136 (ptt-90) REVERT: B 287 ASP cc_start: 0.7136 (t0) cc_final: 0.6829 (m-30) REVERT: C 52 GLN cc_start: 0.8197 (pp30) cc_final: 0.7906 (pp30) REVERT: C 64 TRP cc_start: 0.7800 (t60) cc_final: 0.7269 (t60) REVERT: C 237 ARG cc_start: 0.6766 (ptt180) cc_final: 0.6443 (ptm-80) REVERT: A 52 GLN cc_start: 0.8519 (pm20) cc_final: 0.7894 (pp30) REVERT: A 64 TRP cc_start: 0.7947 (t60) cc_final: 0.7555 (t60) REVERT: H 103 MET cc_start: 0.3474 (OUTLIER) cc_final: 0.2004 (tpp) REVERT: O 63 SER cc_start: 0.1409 (p) cc_final: 0.0426 (m) REVERT: O 121 SER cc_start: 0.3634 (t) cc_final: 0.3311 (p) outliers start: 58 outliers final: 33 residues processed: 204 average time/residue: 0.5102 time to fit residues: 178.6338 Evaluate side-chains 177 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 213 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 196 optimal weight: 30.0000 chunk 276 optimal weight: 4.9990 chunk 413 optimal weight: 7.9990 chunk 437 optimal weight: 20.0000 chunk 216 optimal weight: 0.9990 chunk 391 optimal weight: 50.0000 chunk 118 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 7 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 121 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 641 ASN C 655 HIS C 762 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 655 HIS A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 36927 Z= 0.403 Angle : 0.736 17.579 50217 Z= 0.372 Chirality : 0.049 0.532 5796 Planarity : 0.005 0.061 6419 Dihedral : 6.529 58.763 5898 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 2.16 % Allowed : 8.12 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -2.13 (0.12), residues: 4526 helix: 0.06 (0.19), residues: 679 sheet: -1.47 (0.14), residues: 1296 loop : -1.81 (0.11), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 37 HIS 0.012 0.002 HIS B1083 PHE 0.025 0.003 PHE B 855 TYR 0.032 0.002 TYR A 269 ARG 0.010 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 147 time to evaluate : 4.127 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: N 35 MET cc_start: 0.2572 (ttm) cc_final: 0.2082 (mmm) REVERT: B 52 GLN cc_start: 0.8542 (pm20) cc_final: 0.7780 (pp30) REVERT: B 64 TRP cc_start: 0.7747 (t60) cc_final: 0.7526 (t60) REVERT: B 221 SER cc_start: 0.7318 (OUTLIER) cc_final: 0.6966 (p) REVERT: B 287 ASP cc_start: 0.7910 (t0) cc_final: 0.7252 (m-30) REVERT: C 52 GLN cc_start: 0.8225 (pp30) cc_final: 0.7866 (pp30) REVERT: C 221 SER cc_start: 0.7378 (OUTLIER) cc_final: 0.7031 (p) REVERT: A 52 GLN cc_start: 0.8493 (pm20) cc_final: 0.7775 (pp30) REVERT: A 64 TRP cc_start: 0.8013 (t60) cc_final: 0.7496 (t60) REVERT: A 66 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7353 (m-70) REVERT: H 103 MET cc_start: 0.3305 (OUTLIER) cc_final: 0.2545 (tpt) outliers start: 85 outliers final: 39 residues processed: 225 average time/residue: 0.4582 time to fit residues: 176.7325 Evaluate side-chains 165 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 chunk 373 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 223 optimal weight: 0.9980 chunk 393 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN A 81 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36927 Z= 0.209 Angle : 0.594 13.328 50217 Z= 0.299 Chirality : 0.045 0.560 5796 Planarity : 0.004 0.066 6419 Dihedral : 5.988 59.830 5898 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 1.60 % Allowed : 8.88 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.92 (0.12), residues: 4526 helix: 0.35 (0.20), residues: 690 sheet: -1.38 (0.14), residues: 1316 loop : -1.69 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 152 HIS 0.009 0.001 HIS A 146 PHE 0.019 0.002 PHE N 109 TYR 0.020 0.001 TYR C 170 ARG 0.012 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 134 time to evaluate : 3.852 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: N 35 MET cc_start: 0.2362 (ttm) cc_final: 0.1971 (mmm) REVERT: B 52 GLN cc_start: 0.8532 (pm20) cc_final: 0.7781 (pp30) REVERT: B 221 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.6917 (p) REVERT: B 237 ARG cc_start: 0.6954 (ptm-80) cc_final: 0.6429 (ptt-90) REVERT: B 287 ASP cc_start: 0.7910 (t0) cc_final: 0.7613 (t0) REVERT: C 52 GLN cc_start: 0.8267 (pp30) cc_final: 0.8016 (pp30) REVERT: C 86 PHE cc_start: 0.6276 (t80) cc_final: 0.5944 (t80) REVERT: C 221 SER cc_start: 0.7200 (OUTLIER) cc_final: 0.6864 (p) REVERT: C 1089 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: A 52 GLN cc_start: 0.8497 (pm20) cc_final: 0.7867 (pp30) REVERT: A 64 TRP cc_start: 0.8047 (t60) cc_final: 0.7541 (t60) REVERT: A 66 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7339 (m-70) REVERT: H 103 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.2153 (tpp) outliers start: 63 outliers final: 38 residues processed: 187 average time/residue: 0.4503 time to fit residues: 145.3335 Evaluate side-chains 162 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 1.9990 chunk 394 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 438 optimal weight: 30.0000 chunk 363 optimal weight: 0.0970 chunk 202 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 230 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN A 30 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 36927 Z= 0.263 Angle : 0.606 11.716 50217 Z= 0.307 Chirality : 0.045 0.514 5796 Planarity : 0.004 0.063 6419 Dihedral : 5.782 59.091 5897 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.48 % Favored : 94.43 % Rotamer: Outliers : 1.86 % Allowed : 9.13 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.75 (0.12), residues: 4526 helix: 0.36 (0.20), residues: 695 sheet: -1.22 (0.14), residues: 1306 loop : -1.56 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 152 HIS 0.007 0.002 HIS B 245 PHE 0.061 0.002 PHE B 855 TYR 0.022 0.001 TYR C 269 ARG 0.009 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 128 time to evaluate : 4.249 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: N 35 MET cc_start: 0.2285 (ttm) cc_final: 0.2048 (mmm) REVERT: G 76 ILE cc_start: -0.0355 (OUTLIER) cc_final: -0.0918 (mt) REVERT: B 52 GLN cc_start: 0.8438 (pm20) cc_final: 0.7702 (tm-30) REVERT: B 64 TRP cc_start: 0.8185 (t60) cc_final: 0.7453 (t60) REVERT: B 86 PHE cc_start: 0.5975 (t80) cc_final: 0.5755 (t80) REVERT: B 221 SER cc_start: 0.7232 (OUTLIER) cc_final: 0.6935 (p) REVERT: B 906 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: C 52 GLN cc_start: 0.8249 (pp30) cc_final: 0.7989 (pp30) REVERT: C 221 SER cc_start: 0.7069 (OUTLIER) cc_final: 0.6733 (p) REVERT: C 869 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5788 (mtm) REVERT: C 1029 MET cc_start: 0.6945 (mpp) cc_final: 0.6528 (mpp) REVERT: C 1089 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7508 (m-10) REVERT: C 1146 ASP cc_start: 0.5234 (p0) cc_final: 0.4921 (p0) REVERT: A 52 GLN cc_start: 0.8470 (pm20) cc_final: 0.7799 (pp30) REVERT: A 64 TRP cc_start: 0.8143 (t60) cc_final: 0.7621 (t60) REVERT: A 66 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7601 (m-70) REVERT: H 103 MET cc_start: 0.3070 (OUTLIER) cc_final: 0.2201 (tpp) outliers start: 73 outliers final: 51 residues processed: 188 average time/residue: 0.4384 time to fit residues: 144.9732 Evaluate side-chains 170 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 111 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 112 TRP Chi-restraints excluded: chain N residue 49 MET Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 40.0000 chunk 49 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 247 optimal weight: 0.0870 chunk 368 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 436 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 641 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 36927 Z= 0.168 Angle : 0.559 10.135 50217 Z= 0.282 Chirality : 0.044 0.529 5796 Planarity : 0.004 0.062 6419 Dihedral : 5.435 59.608 5897 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 1.81 % Allowed : 9.57 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.55 (0.12), residues: 4526 helix: 0.53 (0.20), residues: 694 sheet: -1.07 (0.14), residues: 1279 loop : -1.44 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.001 PHE N 109 TYR 0.015 0.001 TYR A 145 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 124 time to evaluate : 4.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 MET cc_start: 0.2252 (ttm) cc_final: 0.2045 (mmm) REVERT: G 76 ILE cc_start: -0.0376 (OUTLIER) cc_final: -0.0956 (mt) REVERT: B 52 GLN cc_start: 0.8418 (pm20) cc_final: 0.7803 (tm-30) REVERT: B 86 PHE cc_start: 0.6060 (t80) cc_final: 0.5855 (t80) REVERT: B 221 SER cc_start: 0.7216 (OUTLIER) cc_final: 0.6880 (p) REVERT: B 237 ARG cc_start: 0.6958 (ptm-80) cc_final: 0.6436 (ptt-90) REVERT: B 906 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: C 52 GLN cc_start: 0.8217 (pp30) cc_final: 0.7960 (pp30) REVERT: C 221 SER cc_start: 0.7147 (OUTLIER) cc_final: 0.6841 (p) REVERT: C 869 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5820 (mtm) REVERT: C 1029 MET cc_start: 0.6984 (tpp) cc_final: 0.6387 (mpp) REVERT: C 1089 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: A 52 GLN cc_start: 0.8419 (pm20) cc_final: 0.7900 (tm-30) REVERT: A 64 TRP cc_start: 0.8108 (t60) cc_final: 0.7617 (t60) REVERT: A 66 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7415 (m-70) REVERT: H 103 MET cc_start: 0.2923 (OUTLIER) cc_final: 0.2451 (tmm) outliers start: 71 outliers final: 44 residues processed: 181 average time/residue: 0.4945 time to fit residues: 156.5489 Evaluate side-chains 169 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 117 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 112 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 260 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 277 optimal weight: 0.6980 chunk 297 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 343 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 ASN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36927 Z= 0.329 Angle : 0.631 11.966 50217 Z= 0.319 Chirality : 0.045 0.475 5796 Planarity : 0.004 0.072 6419 Dihedral : 5.652 58.057 5897 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 2.06 % Allowed : 9.59 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.63 (0.12), residues: 4526 helix: 0.46 (0.20), residues: 677 sheet: -1.17 (0.14), residues: 1307 loop : -1.46 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 64 HIS 0.009 0.002 HIS C 207 PHE 0.054 0.002 PHE B 855 TYR 0.024 0.002 TYR C 269 ARG 0.007 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 122 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 ILE cc_start: -0.0175 (OUTLIER) cc_final: -0.0783 (mt) REVERT: B 52 GLN cc_start: 0.8381 (pm20) cc_final: 0.7794 (tm-30) REVERT: B 86 PHE cc_start: 0.6470 (t80) cc_final: 0.6260 (t80) REVERT: B 221 SER cc_start: 0.7248 (OUTLIER) cc_final: 0.6963 (p) REVERT: B 906 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7585 (m-10) REVERT: C 52 GLN cc_start: 0.8189 (pp30) cc_final: 0.7719 (pp30) REVERT: C 221 SER cc_start: 0.7421 (OUTLIER) cc_final: 0.7144 (p) REVERT: C 239 GLN cc_start: 0.6686 (tt0) cc_final: 0.6305 (tt0) REVERT: C 869 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5845 (mtm) REVERT: C 1089 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7695 (m-10) REVERT: A 52 GLN cc_start: 0.8392 (pm20) cc_final: 0.7841 (pp30) REVERT: A 64 TRP cc_start: 0.8322 (t60) cc_final: 0.7692 (t60) REVERT: A 66 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7474 (m-70) REVERT: A 86 PHE cc_start: 0.6345 (t80) cc_final: 0.5880 (t80) REVERT: A 221 SER cc_start: 0.7148 (OUTLIER) cc_final: 0.6860 (p) REVERT: A 1146 ASP cc_start: 0.5306 (p0) cc_final: 0.5001 (p0) REVERT: H 103 MET cc_start: 0.2874 (OUTLIER) cc_final: 0.2202 (tpp) outliers start: 81 outliers final: 55 residues processed: 187 average time/residue: 0.4202 time to fit residues: 140.7859 Evaluate side-chains 178 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 114 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 112 TRP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 50.0000 chunk 418 optimal weight: 50.0000 chunk 381 optimal weight: 2.9990 chunk 406 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 367 optimal weight: 0.5980 chunk 384 optimal weight: 2.9990 chunk 405 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 ASN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36927 Z= 0.198 Angle : 0.572 11.540 50217 Z= 0.288 Chirality : 0.044 0.486 5796 Planarity : 0.004 0.068 6419 Dihedral : 5.354 59.444 5897 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 1.76 % Allowed : 10.03 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.49 (0.12), residues: 4526 helix: 0.65 (0.21), residues: 677 sheet: -1.08 (0.14), residues: 1276 loop : -1.39 (0.11), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 152 HIS 0.004 0.001 HIS C1048 PHE 0.079 0.002 PHE B 855 TYR 0.017 0.001 TYR A 145 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 123 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 ILE cc_start: -0.0201 (OUTLIER) cc_final: -0.0811 (mt) REVERT: B 52 GLN cc_start: 0.8372 (pm20) cc_final: 0.7921 (tm-30) REVERT: B 221 SER cc_start: 0.7218 (OUTLIER) cc_final: 0.6936 (p) REVERT: B 906 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: C 52 GLN cc_start: 0.8293 (pp30) cc_final: 0.8019 (pp30) REVERT: C 221 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 239 GLN cc_start: 0.6643 (tt0) cc_final: 0.6247 (tt0) REVERT: C 869 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5845 (mtm) REVERT: C 1089 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: A 52 GLN cc_start: 0.8391 (pm20) cc_final: 0.7903 (tm-30) REVERT: A 64 TRP cc_start: 0.8307 (t60) cc_final: 0.7614 (t60) REVERT: A 66 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7384 (m-70) REVERT: A 86 PHE cc_start: 0.6211 (t80) cc_final: 0.5796 (t80) REVERT: A 221 SER cc_start: 0.7150 (OUTLIER) cc_final: 0.6818 (p) REVERT: H 103 MET cc_start: 0.2742 (OUTLIER) cc_final: 0.2321 (tmm) outliers start: 69 outliers final: 55 residues processed: 177 average time/residue: 0.4284 time to fit residues: 133.6087 Evaluate side-chains 178 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 114 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 112 TRP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 7.9990 chunk 430 optimal weight: 50.0000 chunk 262 optimal weight: 0.0980 chunk 204 optimal weight: 3.9990 chunk 299 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 415 optimal weight: 9.9990 chunk 359 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 277 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 ASN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.6340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 36927 Z= 0.407 Angle : 0.685 12.373 50217 Z= 0.349 Chirality : 0.046 0.452 5796 Planarity : 0.005 0.088 6419 Dihedral : 5.804 58.576 5897 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 1.81 % Allowed : 10.20 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.70 (0.12), residues: 4526 helix: 0.35 (0.20), residues: 672 sheet: -1.15 (0.14), residues: 1266 loop : -1.53 (0.11), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 64 HIS 0.009 0.002 HIS B 207 PHE 0.039 0.002 PHE B 855 TYR 0.028 0.002 TYR C 269 ARG 0.006 0.001 ARG C 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 119 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5171 (ppp) cc_final: 0.3504 (ttt) REVERT: G 76 ILE cc_start: -0.0085 (OUTLIER) cc_final: -0.0709 (mt) REVERT: B 52 GLN cc_start: 0.8315 (pm20) cc_final: 0.7930 (tm-30) REVERT: B 221 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6916 (p) REVERT: B 900 MET cc_start: 0.7497 (mmm) cc_final: 0.7024 (mmm) REVERT: B 906 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: C 52 GLN cc_start: 0.8136 (pp30) cc_final: 0.7733 (pp30) REVERT: C 221 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7212 (p) REVERT: C 239 GLN cc_start: 0.6706 (tt0) cc_final: 0.6386 (tt0) REVERT: C 869 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5977 (mtm) REVERT: C 1089 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: A 52 GLN cc_start: 0.8404 (pm20) cc_final: 0.7894 (pp30) REVERT: A 64 TRP cc_start: 0.8444 (t60) cc_final: 0.7789 (t60) REVERT: A 66 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7452 (m-70) REVERT: A 86 PHE cc_start: 0.6389 (t80) cc_final: 0.6061 (t80) REVERT: A 221 SER cc_start: 0.7517 (OUTLIER) cc_final: 0.7206 (p) REVERT: A 869 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5976 (mtm) REVERT: H 103 MET cc_start: 0.2819 (OUTLIER) cc_final: 0.2291 (tpp) REVERT: M 34 MET cc_start: 0.0921 (ppp) cc_final: 0.0365 (ptm) outliers start: 71 outliers final: 56 residues processed: 176 average time/residue: 0.4249 time to fit residues: 132.7473 Evaluate side-chains 176 residues out of total 3953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 110 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 112 TRP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 119 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 1.9990 chunk 382 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 331 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 369 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS M 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.091664 restraints weight = 152387.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.093983 restraints weight = 82435.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.093432 restraints weight = 51188.308| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36927 Z= 0.163 Angle : 0.568 10.682 50217 Z= 0.286 Chirality : 0.043 0.479 5796 Planarity : 0.004 0.081 6419 Dihedral : 5.265 59.259 5897 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.40 % Allowed : 10.71 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.43 (0.12), residues: 4526 helix: 0.69 (0.21), residues: 663 sheet: -1.00 (0.14), residues: 1258 loop : -1.36 (0.11), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 152 HIS 0.006 0.001 HIS B1048 PHE 0.019 0.001 PHE N 109 TYR 0.017 0.001 TYR A 145 ARG 0.006 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5790.95 seconds wall clock time: 108 minutes 25.27 seconds (6505.27 seconds total)