Starting phenix.real_space_refine on Sat Feb 17 07:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lo6_23462/02_2024/7lo6_23462_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 108 5.16 5 Cl 3 4.86 5 C 11302 2.51 5 N 3048 2.21 5 O 3542 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "B TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ARG 419": "NH1" <-> "NH2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 444": "NH1" <-> "NH2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 542": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D ARG 585": "NH1" <-> "NH2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 419": "NH1" <-> "NH2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 97": "NH1" <-> "NH2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 90": "OD1" <-> "OD2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 90": "OD1" <-> "OD2" Residue "L PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18006 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2840 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1026 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2848 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2862 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {'5VG': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" 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 Time building chain proxies: 9.86, per 1000 atoms: 0.55 Number of scatterers: 18006 At special positions: 0 Unit cell: (149.04, 139.104, 156.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 108 16.00 F 3 9.00 O 3542 8.00 N 3048 7.00 C 11302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 385 " distance=2.07 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " ALPHA1-6 " MAN N 4 " - " MAN N 5 " " BMA P 3 " - " MAN P 6 " " BMA S 3 " - " MAN S 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 363 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 295 " " NAG C 603 " - " ASN C 332 " " NAG C 604 " - " ASN C 339 " " NAG C 605 " - " ASN C 355 " " NAG C 606 " - " ASN C 363 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 448 " " NAG D 701 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 332 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 363 " " NAG E 607 " - " ASN E 392 " " NAG E 608 " - " ASN E 448 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN C 234 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 276 " " NAG U 1 " - " ASN E 339 " " NAG V 1 " - " ASN E 386 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.2 seconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 35 sheets defined 17.4% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 removed outlier: 4.425A pdb=" N ALA A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.511A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 4.334A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.928A pdb=" N PHE B 519 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 543 removed outlier: 4.214A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.066A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 623 No H-bonds generated for 'chain 'B' and resid 620 through 623' Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 655 removed outlier: 3.600A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 336 through 352 removed outlier: 3.917A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 478 removed outlier: 3.686A pdb=" N ASN C 478 " --> pdb=" O MET C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 475 through 478' Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.683A pdb=" N PHE D 519 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 525 " --> pdb=" O PHE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 545 removed outlier: 4.749A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 595 removed outlier: 3.985A pdb=" N LEU D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N TRP D 571 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 585 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 595 " --> pdb=" O GLN D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 654 removed outlier: 3.642A pdb=" N GLU D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 removed outlier: 3.924A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.709A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 343 through 352 removed outlier: 3.623A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 526 removed outlier: 4.088A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 540 removed outlier: 3.664A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL F 539 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 573 through 595 removed outlier: 4.418A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 657 removed outlier: 3.851A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.766A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= E, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.041A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.713A pdb=" N VAL A 120 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 424 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 444 through 449 removed outlier: 8.256A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.528A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= J, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.628A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= L, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.576A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS C 239 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 292 through 294 removed outlier: 3.824A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.592A pdb=" N ASN C 332 " --> pdb=" O ASN C 295 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 358 through 361 Processing sheet with id= P, first strand: chain 'C' and resid 374 through 378 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= S, first strand: chain 'E' and resid 91 through 93 removed outlier: 4.030A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 197 through 202 removed outlier: 3.898A pdb=" N SER E 199 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 123 " --> pdb=" O SER E 199 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 120 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 443 through 447 removed outlier: 3.716A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 465 through 469 removed outlier: 6.811A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'G' and resid 85 through 90 removed outlier: 6.010A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.541A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 5 through 7 Processing sheet with id= AB, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.852A pdb=" N ARG I 105 " --> pdb=" O LEU I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'I' and resid 85 through 89 removed outlier: 3.673A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.733A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP J 73 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.929A pdb=" N VAL J 99 " --> pdb=" O SER J 33 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 84 through 86 removed outlier: 3.508A pdb=" N GLN K 38 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS K 39 " --> pdb=" O PRO K 44 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 65 through 67 Processing sheet with id= AH, first strand: chain 'L' and resid 17 through 20 Processing sheet with id= AI, first strand: chain 'L' and resid 92 through 100 removed outlier: 3.952A pdb=" N PHE L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP L 36 " --> pdb=" O GLY L 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA L 40 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU L 45 " --> pdb=" O ALA L 40 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1140 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: 5.62 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2896 1.30 - 1.44: 5184 1.44 - 1.58: 10159 1.58 - 1.71: 0 1.71 - 1.85: 147 Bond restraints: 18386 Sorted by residual: bond pdb=" CA TRP E 96 " pdb=" C TRP E 96 " ideal model delta sigma weight residual 1.523 1.447 0.076 1.80e-02 3.09e+03 1.78e+01 bond pdb=" C CYS E 239 " pdb=" N PRO E 240 " ideal model delta sigma weight residual 1.334 1.303 0.031 8.40e-03 1.42e+04 1.35e+01 bond pdb=" C2 MAN P 4 " pdb=" C3 MAN P 4 " ideal model delta sigma weight residual 1.525 1.461 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N ILE C 449 " pdb=" CA ILE C 449 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.25e-02 6.40e+03 8.73e+00 bond pdb=" CA THR E 71 " pdb=" C THR E 71 " ideal model delta sigma weight residual 1.518 1.402 0.116 4.01e-02 6.22e+02 8.41e+00 ... (remaining 18381 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.92: 392 105.92 - 112.97: 10616 112.97 - 120.02: 5798 120.02 - 127.07: 7906 127.07 - 134.12: 265 Bond angle restraints: 24977 Sorted by residual: angle pdb=" N ALA D 561 " pdb=" CA ALA D 561 " pdb=" C ALA D 561 " ideal model delta sigma weight residual 112.45 119.92 -7.47 1.39e+00 5.18e-01 2.89e+01 angle pdb=" N LEU C 390 " pdb=" CA LEU C 390 " pdb=" C LEU C 390 " ideal model delta sigma weight residual 114.04 108.39 5.65 1.24e+00 6.50e-01 2.08e+01 angle pdb=" C CYS E 54 " pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " ideal model delta sigma weight residual 110.42 101.75 8.67 1.99e+00 2.53e-01 1.90e+01 angle pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " ideal model delta sigma weight residual 114.40 124.22 -9.82 2.30e+00 1.89e-01 1.82e+01 angle pdb=" C ALA E 266 " pdb=" N GLU E 267 " pdb=" CA GLU E 267 " ideal model delta sigma weight residual 122.42 115.11 7.31 1.77e+00 3.19e-01 1.71e+01 ... (remaining 24972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 10846 22.56 - 45.12: 691 45.12 - 67.68: 132 67.68 - 90.24: 38 90.24 - 112.81: 13 Dihedral angle restraints: 11720 sinusoidal: 5412 harmonic: 6308 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -7.65 -78.35 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 385 " pdb=" CB CYS C 385 " ideal model delta sinusoidal sigma weight residual -86.00 -10.01 -75.99 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 331 " pdb=" SG CYS C 331 " pdb=" SG CYS C 418 " pdb=" CB CYS C 418 " ideal model delta sinusoidal sigma weight residual -86.00 -152.11 66.11 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 11717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 2952 0.314 - 0.627: 3 0.627 - 0.941: 1 0.941 - 1.254: 0 1.254 - 1.568: 2 Chirality restraints: 2958 Sorted by residual: chirality pdb=" C1 MAN N 5 " pdb=" O6 MAN N 4 " pdb=" C2 MAN N 5 " pdb=" O5 MAN N 5 " both_signs ideal model delta sigma weight residual False 2.40 0.83 1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 MAN S 6 " pdb=" O6 BMA S 3 " pdb=" C2 MAN S 6 " pdb=" O5 MAN S 6 " both_signs ideal model delta sigma weight residual False 2.40 1.03 1.37 2.00e-02 2.50e+03 4.72e+03 chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.45e+03 ... (remaining 2955 not shown) Planarity restraints: 3139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.325 2.00e-02 2.50e+03 2.76e-01 9.49e+02 pdb=" C7 NAG N 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 608 " -0.285 2.00e-02 2.50e+03 2.40e-01 7.20e+02 pdb=" C7 NAG C 608 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG C 608 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 608 " 0.409 2.00e-02 2.50e+03 pdb=" O7 NAG C 608 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " 0.194 2.00e-02 2.50e+03 1.61e-01 3.22e+02 pdb=" C7 NAG S 1 " -0.055 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " 0.142 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " -0.260 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 3136 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 322 2.54 - 3.13: 15551 3.13 - 3.72: 26183 3.72 - 4.31: 36118 4.31 - 4.90: 59219 Nonbonded interactions: 137393 Sorted by model distance: nonbonded pdb=" O THR E 278 " pdb=" O6 NAG T 1 " model vdw 1.951 2.440 nonbonded pdb=" OG SER A 256 " pdb=" O LEU A 259 " model vdw 2.085 2.440 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.088 2.440 nonbonded pdb=" O THR C 278 " pdb=" O6 NAG Q 1 " model vdw 2.090 2.440 nonbonded pdb=" OG SER I 14 " pdb=" O LYS I 109 " model vdw 2.099 2.440 ... (remaining 137388 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 33 through 397 or resid 412 through 503 or resid 601 throu \ gh 609)) selection = (chain 'C' and (resid 33 through 300 or resid 325 through 397 or resid 412 throu \ gh 503 or resid 601 through 609)) selection = (chain 'E' and (resid 33 through 126 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 300 or resid 325 through 464 or \ (resid 465 and (name N or name CA or name C or name O or name CB or name OG1)) \ or resid 466 through 503 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and (resid 519 through 541 or resid 563 through 654 or (resid 655 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 519 through 541 or (resid 563 and (name N or name CA or na \ me C or name O or name CB )) or resid 564 through 655)) selection = (chain 'F' and (resid 519 through 620 or (resid 621 and (name N or name CA or na \ me C or name O or name CB )) or resid 622 through 654 or (resid 655 and (name N \ or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 104 or (resid 105 and (name N or name CA or name C or name \ O or name CB )) or resid 106 through 111)) selection = (chain 'I' and (resid 1 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 111)) selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 111)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'S' and (resid 2 or resid 5 through 7)) } 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=0.50 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.510 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 50.400 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.170 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.011 0.116 18386 Z= 0.711 Angle : 0.989 13.436 24977 Z= 0.508 Chirality : 0.072 1.568 2958 Planarity : 0.009 0.276 3102 Dihedral : 15.558 112.805 7541 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.87 % Favored : 87.08 % Rotamer: Outliers : 0.64 % Allowed : 8.83 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.14), residues: 2144 helix: -3.61 (0.18), residues: 369 sheet: -3.10 (0.17), residues: 661 loop : -4.01 (0.14), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 479 HIS 0.009 0.002 HIS E 105 PHE 0.026 0.002 PHE E 53 TYR 0.019 0.002 TYR C 384 ARG 0.007 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9221 (tttt) cc_final: 0.8992 (ttmm) REVERT: A 91 GLU cc_start: 0.7267 (tt0) cc_final: 0.7024 (tt0) REVERT: A 103 GLN cc_start: 0.8615 (mt0) cc_final: 0.8383 (mt0) REVERT: A 252 LYS cc_start: 0.9347 (mttt) cc_final: 0.9011 (mtpp) REVERT: A 361 PHE cc_start: 0.6744 (m-80) cc_final: 0.6425 (m-80) REVERT: A 426 MET cc_start: 0.8097 (tpp) cc_final: 0.7704 (tpp) REVERT: A 475 MET cc_start: 0.9019 (mmm) cc_final: 0.8379 (mmm) REVERT: B 535 MET cc_start: 0.9135 (mmm) cc_final: 0.8757 (mmm) REVERT: B 601 LYS cc_start: 0.9445 (mttt) cc_final: 0.9096 (mtmt) REVERT: B 651 ASN cc_start: 0.8796 (m-40) cc_final: 0.8595 (m110) REVERT: D 535 MET cc_start: 0.8790 (mtm) cc_final: 0.8572 (mtm) REVERT: D 591 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9091 (tm-30) REVERT: D 634 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8373 (mt-10) REVERT: E 268 GLU cc_start: 0.7682 (pt0) cc_final: 0.7129 (pt0) REVERT: E 482 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7864 (mm-30) REVERT: F 535 MET cc_start: 0.9101 (mmt) cc_final: 0.8890 (mmm) REVERT: F 621 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8416 (tm-30) REVERT: F 622 ILE cc_start: 0.9008 (mt) cc_final: 0.8491 (mm) REVERT: G 27 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8455 (mm-30) REVERT: G 78 LEU cc_start: 0.8790 (mt) cc_final: 0.8559 (mt) REVERT: H 110 ASP cc_start: 0.8320 (m-30) cc_final: 0.7710 (m-30) REVERT: H 116 LYS cc_start: 0.9081 (tttp) cc_final: 0.8808 (ttmt) REVERT: I 39 LYS cc_start: 0.9033 (mttt) cc_final: 0.8658 (mmmt) REVERT: I 78 LEU cc_start: 0.8760 (mp) cc_final: 0.8507 (mp) REVERT: I 102 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8436 (mp10) REVERT: K 35 TRP cc_start: 0.7118 (m100) cc_final: 0.5965 (m100) REVERT: L 94 TYR cc_start: 0.8731 (m-80) cc_final: 0.8400 (m-80) REVERT: L 112 ASN cc_start: 0.7615 (m110) cc_final: 0.7309 (m110) outliers start: 12 outliers final: 3 residues processed: 286 average time/residue: 0.3633 time to fit residues: 147.3414 Evaluate side-chains 224 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 221 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain F residue 658 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 195 optimal weight: 50.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 352 HIS B 640 GLN B 651 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 103 GLN E 279 ASN E 352 HIS E 422 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18386 Z= 0.219 Angle : 0.709 11.548 24977 Z= 0.338 Chirality : 0.048 0.293 2958 Planarity : 0.004 0.046 3102 Dihedral : 11.652 79.681 3587 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.92 % Allowed : 15.86 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.16), residues: 2144 helix: -2.09 (0.24), residues: 378 sheet: -2.54 (0.18), residues: 667 loop : -3.27 (0.15), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 35 HIS 0.005 0.001 HIS J 63 PHE 0.020 0.001 PHE L 114 TYR 0.011 0.001 TYR D 638 ARG 0.007 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 1.989 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: A 91 GLU cc_start: 0.7199 (tt0) cc_final: 0.6913 (tt0) REVERT: A 252 LYS cc_start: 0.9255 (mttt) cc_final: 0.8889 (mtpp) REVERT: A 384 TYR cc_start: 0.6959 (m-80) cc_final: 0.6728 (m-10) REVERT: A 426 MET cc_start: 0.8266 (tpp) cc_final: 0.7754 (tpp) REVERT: A 435 TYR cc_start: 0.7469 (m-80) cc_final: 0.7233 (m-80) REVERT: A 475 MET cc_start: 0.8919 (mmm) cc_final: 0.8712 (tpp) REVERT: B 601 LYS cc_start: 0.9367 (mttt) cc_final: 0.9018 (mtmt) REVERT: B 605 CYS cc_start: 0.5600 (OUTLIER) cc_final: 0.5334 (p) REVERT: C 100 MET cc_start: 0.8923 (mtp) cc_final: 0.8678 (mtp) REVERT: D 634 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8309 (mt-10) REVERT: D 654 GLU cc_start: 0.7944 (tp30) cc_final: 0.7640 (tp30) REVERT: F 621 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8341 (tm-30) REVERT: F 622 ILE cc_start: 0.8905 (mt) cc_final: 0.8369 (mm) REVERT: G 27 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8559 (mm-30) REVERT: G 36 TYR cc_start: 0.8355 (m-80) cc_final: 0.7877 (m-80) REVERT: G 46 LEU cc_start: 0.9351 (tp) cc_final: 0.8966 (tp) REVERT: H 110 ASP cc_start: 0.8073 (m-30) cc_final: 0.7819 (m-30) REVERT: H 115 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8980 (mt) REVERT: H 116 LYS cc_start: 0.9033 (tttp) cc_final: 0.8783 (ttmt) REVERT: I 47 LEU cc_start: 0.9529 (mt) cc_final: 0.9322 (mp) REVERT: I 78 LEU cc_start: 0.8688 (mp) cc_final: 0.8368 (tp) REVERT: I 102 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8532 (mp10) REVERT: K 36 TYR cc_start: 0.6765 (m-80) cc_final: 0.5261 (m-80) REVERT: K 87 TYR cc_start: 0.6273 (m-10) cc_final: 0.6007 (m-80) REVERT: L 94 TYR cc_start: 0.8678 (m-80) cc_final: 0.8266 (m-80) REVERT: L 109 TYR cc_start: 0.7667 (t80) cc_final: 0.7336 (t80) REVERT: L 115 LEU cc_start: 0.8890 (mt) cc_final: 0.8684 (mm) REVERT: L 116 LYS cc_start: 0.8263 (tptp) cc_final: 0.7903 (tptp) outliers start: 36 outliers final: 19 residues processed: 287 average time/residue: 0.3289 time to fit residues: 137.7552 Evaluate side-chains 257 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 193 optimal weight: 30.0000 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 18386 Z= 0.361 Angle : 0.722 11.414 24977 Z= 0.342 Chirality : 0.048 0.293 2958 Planarity : 0.004 0.045 3102 Dihedral : 10.946 78.180 3584 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.99 % Allowed : 17.03 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.16), residues: 2144 helix: -1.57 (0.25), residues: 374 sheet: -2.38 (0.19), residues: 659 loop : -3.08 (0.16), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 610 HIS 0.004 0.001 HIS E 105 PHE 0.016 0.002 PHE E 53 TYR 0.017 0.002 TYR G 91 ARG 0.006 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 242 time to evaluate : 2.139 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: A 91 GLU cc_start: 0.7171 (tt0) cc_final: 0.6875 (tt0) REVERT: A 252 LYS cc_start: 0.9242 (mttt) cc_final: 0.8912 (mmmm) REVERT: A 426 MET cc_start: 0.8315 (tpp) cc_final: 0.7853 (tpp) REVERT: A 475 MET cc_start: 0.8905 (mmm) cc_final: 0.8394 (mmm) REVERT: B 601 LYS cc_start: 0.9386 (mttt) cc_final: 0.9044 (mtmt) REVERT: B 605 CYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5577 (p) REVERT: B 648 GLU cc_start: 0.9105 (tp30) cc_final: 0.8814 (pp20) REVERT: C 100 MET cc_start: 0.9001 (mtp) cc_final: 0.8767 (mtp) REVERT: D 535 MET cc_start: 0.8724 (mtm) cc_final: 0.8462 (mtm) REVERT: D 591 GLN cc_start: 0.9462 (tm-30) cc_final: 0.9154 (tm-30) REVERT: D 634 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8297 (mt-10) REVERT: D 654 GLU cc_start: 0.7936 (tp30) cc_final: 0.7592 (tp30) REVERT: F 621 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8374 (tm-30) REVERT: F 622 ILE cc_start: 0.8957 (mt) cc_final: 0.8481 (mm) REVERT: G 27 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8559 (mm-30) REVERT: G 36 TYR cc_start: 0.8381 (m-80) cc_final: 0.7886 (m-80) REVERT: G 46 LEU cc_start: 0.9328 (tp) cc_final: 0.8996 (tp) REVERT: H 110 ASP cc_start: 0.8207 (m-30) cc_final: 0.7887 (m-30) REVERT: H 115 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8991 (mt) REVERT: H 116 LYS cc_start: 0.9049 (tttp) cc_final: 0.8807 (ttmt) REVERT: I 4 MET cc_start: 0.6300 (ptt) cc_final: 0.6041 (tmm) REVERT: I 78 LEU cc_start: 0.8652 (mp) cc_final: 0.8298 (mp) REVERT: I 102 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8520 (mp10) REVERT: K 4 MET cc_start: 0.3073 (mtt) cc_final: 0.2509 (mpp) REVERT: K 24 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7568 (tpt170) REVERT: K 36 TYR cc_start: 0.6788 (m-80) cc_final: 0.5244 (m-80) REVERT: K 42 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7200 (mm-40) REVERT: K 87 TYR cc_start: 0.6326 (m-10) cc_final: 0.6004 (m-80) REVERT: L 94 TYR cc_start: 0.8739 (m-80) cc_final: 0.8290 (m-80) REVERT: L 95 PHE cc_start: 0.7641 (m-80) cc_final: 0.7345 (m-80) REVERT: L 109 TYR cc_start: 0.7724 (t80) cc_final: 0.7062 (t80) REVERT: L 115 LEU cc_start: 0.8923 (mt) cc_final: 0.8688 (mm) outliers start: 75 outliers final: 44 residues processed: 298 average time/residue: 0.3260 time to fit residues: 144.2763 Evaluate side-chains 276 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 230 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 HIS Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN L 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18386 Z= 0.178 Angle : 0.648 11.110 24977 Z= 0.304 Chirality : 0.046 0.293 2958 Planarity : 0.004 0.048 3102 Dihedral : 9.770 66.451 3584 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.19 % Allowed : 19.69 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 2144 helix: -1.03 (0.26), residues: 381 sheet: -1.95 (0.20), residues: 653 loop : -2.80 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 35 HIS 0.005 0.001 HIS D 564 PHE 0.010 0.001 PHE C 361 TYR 0.016 0.001 TYR D 638 ARG 0.011 0.000 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 257 time to evaluate : 2.095 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: A 91 GLU cc_start: 0.7217 (tt0) cc_final: 0.6927 (tt0) REVERT: A 252 LYS cc_start: 0.9184 (mttt) cc_final: 0.8915 (mmmm) REVERT: A 426 MET cc_start: 0.8240 (tpp) cc_final: 0.7793 (tpp) REVERT: A 475 MET cc_start: 0.8940 (mmm) cc_final: 0.8448 (mmm) REVERT: B 601 LYS cc_start: 0.9343 (mttt) cc_final: 0.9001 (mtmt) REVERT: B 645 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 648 GLU cc_start: 0.9086 (tp30) cc_final: 0.8781 (pp20) REVERT: C 216 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8063 (p-80) REVERT: D 535 MET cc_start: 0.8757 (mtm) cc_final: 0.8477 (mtm) REVERT: D 591 GLN cc_start: 0.9385 (tm-30) cc_final: 0.9006 (tm-30) REVERT: D 634 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8436 (mt-10) REVERT: E 271 MET cc_start: 0.7165 (mmm) cc_final: 0.6809 (mmm) REVERT: F 535 MET cc_start: 0.8958 (mmm) cc_final: 0.8720 (mmm) REVERT: F 622 ILE cc_start: 0.8919 (mt) cc_final: 0.8446 (mm) REVERT: G 27 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8578 (mm-30) REVERT: G 46 LEU cc_start: 0.9379 (tp) cc_final: 0.9025 (tp) REVERT: H 101 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7189 (mm-30) REVERT: H 115 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9059 (mt) REVERT: H 116 LYS cc_start: 0.9068 (tttp) cc_final: 0.8799 (ttmt) REVERT: I 78 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8334 (tp) REVERT: I 79 GLN cc_start: 0.7963 (mm110) cc_final: 0.7752 (mp10) REVERT: I 102 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8498 (mp10) REVERT: K 4 MET cc_start: 0.3022 (mtt) cc_final: 0.2450 (mpp) REVERT: K 24 ARG cc_start: 0.7846 (ttp-110) cc_final: 0.7644 (tpt170) REVERT: K 35 TRP cc_start: 0.6772 (m100) cc_final: 0.5813 (m100) REVERT: K 36 TYR cc_start: 0.7020 (m-80) cc_final: 0.5626 (m-80) REVERT: K 71 PHE cc_start: 0.7168 (m-10) cc_final: 0.6816 (m-10) REVERT: K 87 TYR cc_start: 0.6273 (m-10) cc_final: 0.6071 (m-80) REVERT: K 100 PHE cc_start: 0.7202 (t80) cc_final: 0.6981 (t80) REVERT: L 31 ARG cc_start: 0.7583 (mmt-90) cc_final: 0.7310 (mmt-90) REVERT: L 94 TYR cc_start: 0.8633 (m-80) cc_final: 0.8263 (m-10) REVERT: L 95 PHE cc_start: 0.7690 (m-80) cc_final: 0.7425 (m-80) REVERT: L 109 TYR cc_start: 0.7729 (t80) cc_final: 0.6916 (t80) REVERT: L 114 PHE cc_start: 0.8141 (p90) cc_final: 0.7931 (p90) REVERT: L 115 LEU cc_start: 0.8979 (mt) cc_final: 0.8698 (mm) outliers start: 60 outliers final: 34 residues processed: 302 average time/residue: 0.3162 time to fit residues: 141.2459 Evaluate side-chains 277 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 239 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN G 6 GLN H 112 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18386 Z= 0.249 Angle : 0.668 11.175 24977 Z= 0.312 Chirality : 0.046 0.287 2958 Planarity : 0.004 0.055 3102 Dihedral : 9.492 64.680 3584 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.15 % Allowed : 19.96 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.17), residues: 2144 helix: -0.74 (0.26), residues: 377 sheet: -1.81 (0.20), residues: 657 loop : -2.68 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 479 HIS 0.006 0.001 HIS L 117 PHE 0.011 0.001 PHE E 53 TYR 0.015 0.001 TYR D 638 ARG 0.012 0.000 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 250 time to evaluate : 2.136 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: A 91 GLU cc_start: 0.7217 (tt0) cc_final: 0.6942 (tt0) REVERT: A 252 LYS cc_start: 0.9214 (mttt) cc_final: 0.8960 (mmmm) REVERT: A 426 MET cc_start: 0.8277 (tpp) cc_final: 0.7807 (tpp) REVERT: A 475 MET cc_start: 0.8955 (mmm) cc_final: 0.8345 (mmm) REVERT: B 535 MET cc_start: 0.9020 (mmt) cc_final: 0.8560 (mmm) REVERT: B 601 LYS cc_start: 0.9347 (mttt) cc_final: 0.9011 (mtmt) REVERT: D 535 MET cc_start: 0.8758 (mtm) cc_final: 0.8462 (mtm) REVERT: D 591 GLN cc_start: 0.9376 (tm-30) cc_final: 0.8979 (tm-30) REVERT: D 634 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8477 (mt-10) REVERT: E 271 MET cc_start: 0.7241 (mmm) cc_final: 0.6855 (mmm) REVERT: G 27 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8608 (mm-30) REVERT: G 46 LEU cc_start: 0.9338 (tp) cc_final: 0.8929 (tp) REVERT: H 115 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8999 (mt) REVERT: H 116 LYS cc_start: 0.9048 (tttp) cc_final: 0.8783 (ttmt) REVERT: I 78 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8351 (tp) REVERT: I 102 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8501 (mp10) REVERT: K 4 MET cc_start: 0.3295 (mtt) cc_final: 0.2724 (mpp) REVERT: K 36 TYR cc_start: 0.7184 (m-80) cc_final: 0.5827 (m-80) REVERT: K 37 GLN cc_start: 0.6623 (tt0) cc_final: 0.6369 (tt0) REVERT: K 46 LEU cc_start: 0.7846 (tt) cc_final: 0.7500 (tt) REVERT: K 86 TYR cc_start: 0.7962 (m-80) cc_final: 0.7644 (m-80) REVERT: K 87 TYR cc_start: 0.6299 (m-10) cc_final: 0.5853 (m-80) REVERT: L 94 TYR cc_start: 0.8647 (m-80) cc_final: 0.8315 (m-10) REVERT: L 95 PHE cc_start: 0.7684 (m-80) cc_final: 0.7415 (m-80) REVERT: L 109 TYR cc_start: 0.7697 (t80) cc_final: 0.6958 (t80) outliers start: 78 outliers final: 53 residues processed: 308 average time/residue: 0.3201 time to fit residues: 147.3148 Evaluate side-chains 288 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 279 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18386 Z= 0.227 Angle : 0.664 11.078 24977 Z= 0.311 Chirality : 0.046 0.286 2958 Planarity : 0.004 0.050 3102 Dihedral : 9.236 60.775 3584 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.04 % Allowed : 20.86 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 2144 helix: -0.53 (0.27), residues: 378 sheet: -1.74 (0.20), residues: 664 loop : -2.55 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP L 47 HIS 0.004 0.001 HIS L 117 PHE 0.041 0.002 PHE K 100 TYR 0.011 0.001 TYR D 638 ARG 0.013 0.000 ARG G 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 2.267 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: A 91 GLU cc_start: 0.7195 (tt0) cc_final: 0.6943 (tt0) REVERT: A 252 LYS cc_start: 0.9196 (mttt) cc_final: 0.8982 (mmmm) REVERT: A 416 LEU cc_start: 0.9265 (mp) cc_final: 0.8750 (tp) REVERT: A 426 MET cc_start: 0.8267 (tpp) cc_final: 0.7797 (tpp) REVERT: A 475 MET cc_start: 0.8973 (mmm) cc_final: 0.8465 (mmm) REVERT: B 535 MET cc_start: 0.9087 (mmt) cc_final: 0.8616 (mmm) REVERT: B 575 GLN cc_start: 0.8639 (mt0) cc_final: 0.8437 (mt0) REVERT: B 601 LYS cc_start: 0.9341 (mttt) cc_final: 0.9008 (mtmt) REVERT: D 535 MET cc_start: 0.8741 (mtm) cc_final: 0.8429 (mtm) REVERT: D 591 GLN cc_start: 0.9370 (tm-30) cc_final: 0.8967 (tm-30) REVERT: E 271 MET cc_start: 0.7308 (mmm) cc_final: 0.6915 (mmm) REVERT: E 285 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8748 (mp) REVERT: G 27 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8597 (mm-30) REVERT: G 46 LEU cc_start: 0.9337 (tp) cc_final: 0.8924 (tp) REVERT: G 97 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8115 (mtp-110) REVERT: H 115 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8990 (mt) REVERT: H 116 LYS cc_start: 0.9057 (tttp) cc_final: 0.8752 (ttmt) REVERT: I 78 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8346 (mp) REVERT: I 102 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8678 (mp10) REVERT: K 4 MET cc_start: 0.3232 (mtt) cc_final: 0.2519 (mpp) REVERT: K 36 TYR cc_start: 0.7085 (m-80) cc_final: 0.5874 (m-80) REVERT: K 37 GLN cc_start: 0.6614 (tt0) cc_final: 0.6399 (tt0) REVERT: K 49 TYR cc_start: 0.4658 (p90) cc_final: 0.4428 (p90) REVERT: K 87 TYR cc_start: 0.6108 (m-10) cc_final: 0.5712 (m-80) REVERT: L 94 TYR cc_start: 0.8650 (m-80) cc_final: 0.8309 (m-10) REVERT: L 95 PHE cc_start: 0.7667 (m-80) cc_final: 0.7404 (m-80) REVERT: L 115 LEU cc_start: 0.8756 (mm) cc_final: 0.8298 (mm) outliers start: 76 outliers final: 59 residues processed: 306 average time/residue: 0.3138 time to fit residues: 144.4284 Evaluate side-chains 293 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN L 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18386 Z= 0.210 Angle : 0.652 11.371 24977 Z= 0.303 Chirality : 0.046 0.282 2958 Planarity : 0.004 0.049 3102 Dihedral : 8.899 59.852 3584 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.99 % Allowed : 21.13 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.17), residues: 2144 helix: -0.42 (0.27), residues: 376 sheet: -1.66 (0.20), residues: 670 loop : -2.40 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 47 HIS 0.004 0.001 HIS L 117 PHE 0.023 0.001 PHE K 100 TYR 0.011 0.001 TYR D 638 ARG 0.008 0.000 ARG G 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 249 time to evaluate : 2.395 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: A 91 GLU cc_start: 0.7185 (tt0) cc_final: 0.6930 (tt0) REVERT: A 252 LYS cc_start: 0.9206 (mttt) cc_final: 0.8985 (mmmm) REVERT: A 416 LEU cc_start: 0.9261 (mp) cc_final: 0.8761 (tp) REVERT: A 426 MET cc_start: 0.8259 (tpp) cc_final: 0.7788 (tpp) REVERT: A 475 MET cc_start: 0.8938 (mmm) cc_final: 0.8351 (mmm) REVERT: B 535 MET cc_start: 0.9103 (mmt) cc_final: 0.8643 (mmm) REVERT: B 601 LYS cc_start: 0.9332 (mttt) cc_final: 0.8987 (mtmt) REVERT: D 535 MET cc_start: 0.8790 (mtm) cc_final: 0.8481 (mtm) REVERT: D 591 GLN cc_start: 0.9371 (tm-30) cc_final: 0.8932 (tm-30) REVERT: E 271 MET cc_start: 0.7292 (mmm) cc_final: 0.6911 (mmm) REVERT: E 285 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8748 (mp) REVERT: E 475 MET cc_start: 0.9230 (mmm) cc_final: 0.8915 (mmm) REVERT: E 492 GLU cc_start: 0.8272 (pp20) cc_final: 0.7593 (pp20) REVERT: G 27 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8590 (mm-30) REVERT: G 46 LEU cc_start: 0.9347 (tp) cc_final: 0.9096 (tp) REVERT: G 97 ARG cc_start: 0.8849 (ttm110) cc_final: 0.8359 (mtp85) REVERT: H 10 GLU cc_start: 0.8250 (tp30) cc_final: 0.7768 (tm-30) REVERT: H 85 ASN cc_start: 0.8109 (t0) cc_final: 0.7258 (p0) REVERT: H 116 LYS cc_start: 0.9051 (tttp) cc_final: 0.8749 (ttmt) REVERT: I 78 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8288 (tp) REVERT: I 102 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8614 (mp10) REVERT: K 4 MET cc_start: 0.2999 (mtt) cc_final: 0.2573 (mpp) REVERT: K 36 TYR cc_start: 0.7155 (m-80) cc_final: 0.5909 (m-80) REVERT: K 45 ARG cc_start: 0.8670 (tpt-90) cc_final: 0.8456 (tpt-90) REVERT: K 46 LEU cc_start: 0.7943 (tt) cc_final: 0.7515 (tt) REVERT: K 87 TYR cc_start: 0.6108 (m-10) cc_final: 0.5672 (m-80) REVERT: K 100 PHE cc_start: 0.7199 (t80) cc_final: 0.6723 (t80) REVERT: L 31 ARG cc_start: 0.7731 (mmt-90) cc_final: 0.7482 (mmt-90) REVERT: L 94 TYR cc_start: 0.8655 (m-80) cc_final: 0.8331 (m-10) REVERT: L 95 PHE cc_start: 0.7665 (m-80) cc_final: 0.7408 (m-80) REVERT: L 115 LEU cc_start: 0.8689 (mm) cc_final: 0.8179 (mm) outliers start: 75 outliers final: 57 residues processed: 307 average time/residue: 0.3101 time to fit residues: 142.6727 Evaluate side-chains 291 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 232 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 0.0170 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18386 Z= 0.216 Angle : 0.658 11.209 24977 Z= 0.306 Chirality : 0.046 0.281 2958 Planarity : 0.004 0.049 3102 Dihedral : 8.710 59.821 3584 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.67 % Allowed : 22.35 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.18), residues: 2144 helix: -0.28 (0.27), residues: 376 sheet: -1.54 (0.20), residues: 664 loop : -2.35 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 47 HIS 0.004 0.001 HIS J 63 PHE 0.014 0.001 PHE K 100 TYR 0.009 0.001 TYR K 87 ARG 0.009 0.000 ARG J 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 241 time to evaluate : 2.097 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: A 91 GLU cc_start: 0.7188 (tt0) cc_final: 0.6924 (tt0) REVERT: A 252 LYS cc_start: 0.9206 (mttt) cc_final: 0.8984 (mmmm) REVERT: A 416 LEU cc_start: 0.9262 (mp) cc_final: 0.8758 (tp) REVERT: A 426 MET cc_start: 0.8249 (tpp) cc_final: 0.7775 (tpp) REVERT: A 475 MET cc_start: 0.8940 (mmm) cc_final: 0.8336 (mmm) REVERT: B 535 MET cc_start: 0.9131 (mmt) cc_final: 0.8634 (mmm) REVERT: B 601 LYS cc_start: 0.9336 (mttt) cc_final: 0.8983 (mtmt) REVERT: D 535 MET cc_start: 0.8788 (mtm) cc_final: 0.8485 (mtm) REVERT: D 626 MET cc_start: 0.6613 (ttp) cc_final: 0.6400 (ttp) REVERT: E 271 MET cc_start: 0.7279 (mmm) cc_final: 0.7065 (mmm) REVERT: E 285 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8749 (mp) REVERT: E 492 GLU cc_start: 0.8266 (pp20) cc_final: 0.7578 (pp20) REVERT: G 18 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7549 (mmm160) REVERT: G 27 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8597 (mm-30) REVERT: G 46 LEU cc_start: 0.9380 (tp) cc_final: 0.9104 (tp) REVERT: G 97 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8390 (mtp85) REVERT: H 116 LYS cc_start: 0.9047 (tttp) cc_final: 0.8765 (ttmt) REVERT: I 78 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8265 (tp) REVERT: I 102 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8743 (mp10) REVERT: J 48 MET cc_start: 0.8386 (mmm) cc_final: 0.8119 (mmm) REVERT: K 4 MET cc_start: 0.3078 (mtt) cc_final: 0.2654 (mpp) REVERT: K 36 TYR cc_start: 0.7228 (m-80) cc_final: 0.6164 (m-80) REVERT: K 46 LEU cc_start: 0.8147 (tt) cc_final: 0.7760 (tt) REVERT: K 87 TYR cc_start: 0.6112 (m-10) cc_final: 0.5701 (m-80) REVERT: K 100 PHE cc_start: 0.7187 (t80) cc_final: 0.6673 (t80) REVERT: L 94 TYR cc_start: 0.8575 (m-80) cc_final: 0.8372 (m-10) REVERT: L 95 PHE cc_start: 0.7693 (m-80) cc_final: 0.7441 (m-80) REVERT: L 115 LEU cc_start: 0.8772 (mm) cc_final: 0.8334 (mm) outliers start: 69 outliers final: 63 residues processed: 296 average time/residue: 0.3128 time to fit residues: 137.8423 Evaluate side-chains 294 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 229 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 30.0000 chunk 181 optimal weight: 0.0670 chunk 193 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 192 optimal weight: 0.0670 chunk 126 optimal weight: 0.9980 overall best weight: 1.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18386 Z= 0.191 Angle : 0.654 10.954 24977 Z= 0.303 Chirality : 0.045 0.276 2958 Planarity : 0.004 0.049 3102 Dihedral : 8.364 59.830 3584 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.57 % Allowed : 22.57 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.18), residues: 2144 helix: -0.13 (0.28), residues: 375 sheet: -1.43 (0.21), residues: 656 loop : -2.19 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 631 HIS 0.004 0.001 HIS J 63 PHE 0.022 0.001 PHE F 519 TYR 0.009 0.001 TYR K 87 ARG 0.007 0.000 ARG J 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 244 time to evaluate : 2.265 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: A 91 GLU cc_start: 0.7210 (tt0) cc_final: 0.6954 (tt0) REVERT: A 252 LYS cc_start: 0.9191 (mttt) cc_final: 0.8980 (mmmm) REVERT: A 416 LEU cc_start: 0.9261 (mp) cc_final: 0.8774 (tp) REVERT: A 426 MET cc_start: 0.8213 (tpp) cc_final: 0.7742 (tpp) REVERT: A 475 MET cc_start: 0.8955 (mmm) cc_final: 0.8376 (mmm) REVERT: B 535 MET cc_start: 0.9093 (mmt) cc_final: 0.8623 (mmp) REVERT: B 601 LYS cc_start: 0.9337 (mttt) cc_final: 0.8986 (mtmt) REVERT: B 648 GLU cc_start: 0.9060 (tp30) cc_final: 0.8752 (pp20) REVERT: C 369 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8993 (tt) REVERT: D 535 MET cc_start: 0.8811 (mtm) cc_final: 0.8487 (mtm) REVERT: E 285 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8752 (mp) REVERT: E 475 MET cc_start: 0.9194 (mmm) cc_final: 0.8972 (mmm) REVERT: E 492 GLU cc_start: 0.8235 (pp20) cc_final: 0.7538 (pp20) REVERT: G 18 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7675 (mmm160) REVERT: G 27 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8636 (mm-30) REVERT: G 97 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8535 (mtp85) REVERT: H 10 GLU cc_start: 0.8257 (tp30) cc_final: 0.7798 (tm-30) REVERT: H 85 ASN cc_start: 0.8094 (t0) cc_final: 0.7265 (p0) REVERT: H 116 LYS cc_start: 0.9033 (tttp) cc_final: 0.8756 (ttmt) REVERT: I 36 TYR cc_start: 0.8319 (m-80) cc_final: 0.8004 (m-80) REVERT: I 78 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8245 (tp) REVERT: I 102 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8769 (mp10) REVERT: J 48 MET cc_start: 0.8410 (mmm) cc_final: 0.8129 (mmm) REVERT: J 116 LYS cc_start: 0.9335 (tppp) cc_final: 0.8999 (tppt) REVERT: K 4 MET cc_start: 0.3088 (mtt) cc_final: 0.2703 (mpp) REVERT: K 36 TYR cc_start: 0.7288 (m-80) cc_final: 0.6196 (m-80) REVERT: K 45 ARG cc_start: 0.8746 (tpt-90) cc_final: 0.8446 (tpt-90) REVERT: K 46 LEU cc_start: 0.7828 (tt) cc_final: 0.7352 (tt) REVERT: K 87 TYR cc_start: 0.6111 (m-10) cc_final: 0.5695 (m-80) REVERT: K 100 PHE cc_start: 0.7265 (t80) cc_final: 0.6749 (t80) REVERT: L 95 PHE cc_start: 0.7738 (m-80) cc_final: 0.7479 (m-80) REVERT: L 115 LEU cc_start: 0.8743 (mm) cc_final: 0.8281 (mm) outliers start: 67 outliers final: 56 residues processed: 296 average time/residue: 0.3240 time to fit residues: 142.6670 Evaluate side-chains 289 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18386 Z= 0.222 Angle : 0.670 11.053 24977 Z= 0.310 Chirality : 0.046 0.278 2958 Planarity : 0.004 0.049 3102 Dihedral : 8.306 59.418 3584 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.46 % Allowed : 22.78 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.18), residues: 2144 helix: -0.08 (0.27), residues: 377 sheet: -1.41 (0.21), residues: 661 loop : -2.19 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 631 HIS 0.004 0.001 HIS J 63 PHE 0.010 0.001 PHE C 53 TYR 0.026 0.001 TYR L 94 ARG 0.008 0.000 ARG J 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 234 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7277 (tt0) cc_final: 0.7017 (tt0) REVERT: A 252 LYS cc_start: 0.9199 (mttt) cc_final: 0.8943 (mmmm) REVERT: A 416 LEU cc_start: 0.9263 (mp) cc_final: 0.8781 (tp) REVERT: A 426 MET cc_start: 0.8232 (tpp) cc_final: 0.7749 (tpp) REVERT: A 475 MET cc_start: 0.8931 (mmm) cc_final: 0.8265 (mmm) REVERT: B 535 MET cc_start: 0.9094 (mmt) cc_final: 0.8624 (mmp) REVERT: B 567 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8747 (mtmt) REVERT: B 601 LYS cc_start: 0.9371 (mttt) cc_final: 0.9004 (mtmt) REVERT: B 648 GLU cc_start: 0.9038 (tp30) cc_final: 0.8762 (pp20) REVERT: C 369 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8991 (tt) REVERT: D 535 MET cc_start: 0.8826 (mtm) cc_final: 0.8543 (mtm) REVERT: E 64 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: E 285 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8748 (mp) REVERT: E 475 MET cc_start: 0.9218 (mmm) cc_final: 0.8954 (mmm) REVERT: E 492 GLU cc_start: 0.8264 (pp20) cc_final: 0.7570 (pp20) REVERT: G 97 ARG cc_start: 0.8878 (ttm110) cc_final: 0.8386 (mtp85) REVERT: H 10 GLU cc_start: 0.8319 (tp30) cc_final: 0.7813 (tm-30) REVERT: H 85 ASN cc_start: 0.8105 (t0) cc_final: 0.7280 (p0) REVERT: H 116 LYS cc_start: 0.9004 (tttp) cc_final: 0.8725 (ttmt) REVERT: I 36 TYR cc_start: 0.8343 (m-80) cc_final: 0.8030 (m-80) REVERT: I 78 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8458 (mp) REVERT: I 102 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8787 (mp10) REVERT: J 48 MET cc_start: 0.8460 (mmm) cc_final: 0.8178 (mmm) REVERT: J 116 LYS cc_start: 0.9359 (tppp) cc_final: 0.9126 (tppt) REVERT: K 4 MET cc_start: 0.3078 (mtt) cc_final: 0.2698 (mpp) REVERT: K 36 TYR cc_start: 0.7302 (m-80) cc_final: 0.6233 (m-80) REVERT: K 49 TYR cc_start: 0.5198 (p90) cc_final: 0.4845 (p90) REVERT: K 87 TYR cc_start: 0.6142 (m-10) cc_final: 0.5732 (m-80) REVERT: K 100 PHE cc_start: 0.7275 (t80) cc_final: 0.6765 (t80) REVERT: L 95 PHE cc_start: 0.7574 (m-80) cc_final: 0.7350 (m-80) REVERT: L 115 LEU cc_start: 0.8773 (mm) cc_final: 0.8338 (mm) outliers start: 65 outliers final: 59 residues processed: 285 average time/residue: 0.3156 time to fit residues: 134.1618 Evaluate side-chains 295 residues out of total 1890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 232 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 328 GLN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 392 ASN Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 1 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.064655 restraints weight = 55162.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065026 restraints weight = 32116.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.065466 restraints weight = 22051.679| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18386 Z= 0.388 Angle : 0.744 12.463 24977 Z= 0.347 Chirality : 0.048 0.306 2958 Planarity : 0.004 0.048 3102 Dihedral : 8.830 59.987 3584 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.57 % Allowed : 22.57 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 2144 helix: -0.26 (0.27), residues: 379 sheet: -1.54 (0.20), residues: 666 loop : -2.29 (0.17), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 631 HIS 0.007 0.001 HIS L 117 PHE 0.015 0.002 PHE C 53 TYR 0.026 0.002 TYR L 94 ARG 0.006 0.000 ARG G 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.72 seconds wall clock time: 67 minutes 25.38 seconds (4045.38 seconds total)