Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 13:25:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txd_26157/08_2023/7txd_26157.pdb" } resolution = 3.87 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= 0.004 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 12854 2.51 5 N 3463 2.21 5 O 4133 1.98 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 ASP 57": "OD1" <-> "OD2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 10": "OD1" <-> "OD2" Residue "I ASP 56": "OD1" <-> "OD2" Residue "I GLU 87": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J ASP 95": "OD1" <-> "OD2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 141": "OD1" <-> "OD2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20555 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "B" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1004 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "D" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 900 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3101 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 22, 'TRANS': 374} Chain breaks: 2 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 965 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "H" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "J" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "K" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "L" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1002 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "M" 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 chiralities: 7 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" 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 chiralities: 7 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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 chiralities: 2 Chain: "h" 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 chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.75, per 1000 atoms: 0.52 Number of scatterers: 20555 At special positions: 0 Unit cell: (126.26, 188.32, 185.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 4133 8.00 N 3463 7.00 C 12854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 16 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 130 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 130 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Simple disulfide: pdb=" SG CYS I 130 " - pdb=" SG CYS I 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA V 3 " - " MAN V 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " BMA V 3 " - " MAN V 5 " " BMA b 3 " - " MAN b 7 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG 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 T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 295 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 462 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG C 601 " - " ASN C 355 " " NAG C 602 " - " ASN C 339 " " NAG C 603 " - " ASN C 88 " " NAG C 604 " - " ASN C 295 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 301 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG D 703 " - " ASN D 618 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 332 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 462 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 339 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 363 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 234 " " NAG S 1 " - " ASN A 355 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 262 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 448 " " NAG Y 1 " - " ASN C 276 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN E 262 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 448 " " NAG e 1 " - " ASN E 276 " " NAG f 1 " - " ASN E 363 " " NAG g 1 " - " ASN E 392 " " NAG h 1 " - " ASN F 611 " Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 3.1 seconds 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 35 sheets defined 31.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 100 through 116 removed outlier: 4.557A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.687A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 removed outlier: 4.047A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.853A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.502A pdb=" N THR B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 removed outlier: 4.088A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.295A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.952A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'C' and resid 64 through 74 Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.868A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.597A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 474 through 481 removed outlier: 3.639A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.717A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 594 removed outlier: 3.714A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.164A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.529A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 655 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.732A pdb=" N GLN E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 327 removed outlier: 3.513A pdb=" N ILE E 326 " --> pdb=" O ILE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.650A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 483 removed outlier: 3.654A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 523 removed outlier: 3.835A pdb=" N LEU F 523 " --> pdb=" O PHE F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 519 through 523' Processing helix chain 'F' and resid 529 through 542 removed outlier: 3.852A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 596 Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.612A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.670A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 657 removed outlier: 3.663A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.569A pdb=" N LEU G 61 " --> pdb=" O ARG G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 79 removed outlier: 3.550A pdb=" N SER G 79 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.602A pdb=" N TRP H 62 " --> pdb=" O ARG H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 79 removed outlier: 3.556A pdb=" N ASP H 78 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 75 through 79' Processing helix chain 'H' and resid 150 through 154 removed outlier: 3.510A pdb=" N SER H 154 " --> pdb=" O LEU H 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.698A pdb=" N LEU I 61 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP I 62 " --> pdb=" O ARG I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 62' Processing helix chain 'I' and resid 75 through 79 Processing helix chain 'I' and resid 150 through 154 removed outlier: 3.511A pdb=" N SER I 154 " --> pdb=" O LEU I 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 Processing helix chain 'J' and resid 49 through 60 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.849A pdb=" N LEU J 76 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 105 through 113 removed outlier: 3.575A pdb=" N LYS J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 138 through 146 Processing helix chain 'J' and resid 148 through 161 removed outlier: 3.761A pdb=" N ALA J 152 " --> pdb=" O ASN J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 47 removed outlier: 3.748A pdb=" N LEU K 43 " --> pdb=" O THR K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 removed outlier: 3.797A pdb=" N VAL K 53 " --> pdb=" O HIS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.634A pdb=" N LEU K 76 " --> pdb=" O THR K 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.524A pdb=" N VAL K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 113 removed outlier: 4.094A pdb=" N LYS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 126 Processing helix chain 'K' and resid 138 through 146 Processing helix chain 'K' and resid 148 through 161 removed outlier: 3.589A pdb=" N ALA K 152 " --> pdb=" O ASN K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 Processing helix chain 'L' and resid 49 through 60 removed outlier: 3.567A pdb=" N VAL L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.596A pdb=" N LEU L 76 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET L 80 " --> pdb=" O LEU L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 92 removed outlier: 3.716A pdb=" N VAL L 86 " --> pdb=" O HIS L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 113 removed outlier: 3.533A pdb=" N LEU L 109 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 113 " --> pdb=" O LEU L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 125 Processing helix chain 'L' and resid 138 through 146 Processing helix chain 'L' and resid 148 through 161 removed outlier: 3.506A pdb=" N ALA L 152 " --> pdb=" O ASN L 148 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL L 154 " --> pdb=" O ASP L 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.091A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.733A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 378 Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 3.567A pdb=" N THR C 37 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.862A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.004A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 196 through 202 removed outlier: 3.590A pdb=" N LEU C 125 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 424 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.508A pdb=" N GLN C 287 " --> pdb=" O MET C 271 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 259 through 260 removed outlier: 4.407A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.638A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 296 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.194A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.885A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 196 through 202 Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 260 removed outlier: 3.727A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.293A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 366 through 367 removed outlier: 3.670A pdb=" N GLY E 366 " --> pdb=" O LYS I 46 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 374 through 378 Processing sheet with id=AC6, first strand: chain 'G' and resid 2 through 5 removed outlier: 4.236A pdb=" N LYS G 2 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G 28 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN G 40 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 43 " --> pdb=" O GLN G 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 12 through 14 removed outlier: 3.637A pdb=" N VAL G 12 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 71 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.346A pdb=" N GLN G 112 " --> pdb=" O GLN G 148 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN G 148 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 131 Processing sheet with id=AD1, first strand: chain 'H' and resid 2 through 5 removed outlier: 4.213A pdb=" N LYS H 2 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS H 29 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP H 28 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN H 40 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 43 " --> pdb=" O GLN H 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AD3, first strand: chain 'H' and resid 99 through 102 removed outlier: 3.511A pdb=" N GLY H 99 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN H 112 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN H 148 " --> pdb=" O GLN H 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AD5, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.057A pdb=" N LYS I 2 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS I 29 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP I 28 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 55 through 56 Processing sheet with id=AD7, first strand: chain 'I' and resid 99 through 102 Processing sheet with id=AD8, first strand: chain 'I' and resid 138 through 139 724 hydrogen bonds defined for protein. 1977 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: 6.86 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6568 1.35 - 1.50: 5501 1.50 - 1.65: 8710 1.65 - 1.80: 44 1.80 - 1.94: 94 Bond restraints: 20917 Sorted by residual: bond pdb=" CB CYS A 331 " pdb=" SG CYS A 331 " ideal model delta sigma weight residual 1.808 1.945 -0.137 3.30e-02 9.18e+02 1.72e+01 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C3 BMA V 3 " pdb=" O3 BMA V 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" N LYS A 502 " pdb=" CA LYS A 502 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 1.808 1.705 0.103 3.30e-02 9.18e+02 9.76e+00 ... (remaining 20912 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.89: 664 106.89 - 114.48: 12961 114.48 - 122.07: 10398 122.07 - 129.66: 4177 129.66 - 137.25: 180 Bond angle restraints: 28380 Sorted by residual: angle pdb=" CA CYS A 296 " pdb=" CB CYS A 296 " pdb=" SG CYS A 296 " ideal model delta sigma weight residual 114.40 137.25 -22.85 2.30e+00 1.89e-01 9.87e+01 angle pdb=" CA ASN C 99 " pdb=" CB ASN C 99 " pdb=" CG ASN C 99 " ideal model delta sigma weight residual 112.60 106.74 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" N CYS A 296 " pdb=" CA CYS A 296 " pdb=" C CYS A 296 " ideal model delta sigma weight residual 108.99 118.12 -9.13 1.57e+00 4.06e-01 3.38e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.48 -13.08 2.30e+00 1.89e-01 3.24e+01 angle pdb=" N ASN A 99 " pdb=" CA ASN A 99 " pdb=" C ASN A 99 " ideal model delta sigma weight residual 113.18 106.84 6.34 1.21e+00 6.83e-01 2.75e+01 ... (remaining 28375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 10923 18.19 - 36.38: 800 36.38 - 54.56: 126 54.56 - 72.75: 23 72.75 - 90.94: 26 Dihedral angle restraints: 11898 sinusoidal: 4784 harmonic: 7114 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -168.98 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.11 -73.11 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 165.00 -72.00 1 1.00e+01 1.00e-02 6.63e+01 ... (remaining 11895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3058 0.090 - 0.180: 426 0.180 - 0.269: 39 0.269 - 0.359: 13 0.359 - 0.449: 5 Chirality restraints: 3541 Sorted by residual: chirality pdb=" CB ILE F 603 " pdb=" CA ILE F 603 " pdb=" CG1 ILE F 603 " pdb=" CG2 ILE F 603 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.44e+00 chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 392 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3538 not shown) Planarity restraints: 3551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 1 " -0.261 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG h 1 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG h 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG h 1 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG h 1 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 703 " 0.167 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG F 703 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG F 703 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG F 703 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG F 703 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG h 2 " -0.096 2.00e-02 2.50e+03 7.97e-02 7.94e+01 pdb=" C7 NAG h 2 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG h 2 " -0.073 2.00e-02 2.50e+03 pdb=" N2 NAG h 2 " 0.127 2.00e-02 2.50e+03 pdb=" O7 NAG h 2 " 0.016 2.00e-02 2.50e+03 ... (remaining 3548 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5118 2.81 - 3.33: 17730 3.33 - 3.85: 32834 3.85 - 4.38: 35559 4.38 - 4.90: 62132 Nonbonded interactions: 153373 Sorted by model distance: nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.287 2.440 nonbonded pdb=" OG SER A 365 " pdb=" O LYS G 46 " model vdw 2.301 2.440 nonbonded pdb=" OD2 ASP C 107 " pdb=" OH TYR C 217 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" O CYS B 604 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.311 2.440 ... (remaining 153368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 33 through 504 or resid 601 through 606)) selection = (chain 'E' and (resid 33 through 504 or resid 601 through 606)) } ncs_group { reference = (chain 'B' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) selection = chain 'D' selection = (chain 'F' and ((resid 522 through 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 542 or resid 564 through 655 or resid 701 t \ hrough 703)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.920 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 55.570 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.006 0.137 20917 Z= 0.381 Angle : 1.056 22.845 28380 Z= 0.540 Chirality : 0.062 0.449 3541 Planarity : 0.008 0.222 3499 Dihedral : 13.232 90.940 7180 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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: -2.19 (0.15), residues: 2441 helix: -1.69 (0.17), residues: 682 sheet: -0.32 (0.24), residues: 475 loop : -1.74 (0.15), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3079 time to fit residues: 176.1433 Evaluate side-chains 247 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 590 GLN C 114 GLN C 197 ASN C 258 GLN C 425 ASN G 129 GLN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.074 20917 Z= 0.458 Angle : 0.777 11.719 28380 Z= 0.391 Chirality : 0.048 0.326 3541 Planarity : 0.005 0.053 3499 Dihedral : 4.719 23.984 2591 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.16), residues: 2441 helix: -0.21 (0.19), residues: 692 sheet: -0.56 (0.23), residues: 467 loop : -1.52 (0.15), residues: 1282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 250 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 280 average time/residue: 0.2961 time to fit residues: 131.9268 Evaluate side-chains 248 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1818 time to fit residues: 16.0420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 0.0270 chunk 182 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 overall best weight: 1.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 543 ASN C 425 ASN D 591 GLN I 52 ASN ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 20917 Z= 0.255 Angle : 0.610 11.013 28380 Z= 0.305 Chirality : 0.044 0.312 3541 Planarity : 0.004 0.049 3499 Dihedral : 4.394 23.876 2591 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2441 helix: 0.32 (0.20), residues: 696 sheet: -0.41 (0.22), residues: 519 loop : -1.43 (0.16), residues: 1226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 278 average time/residue: 0.2965 time to fit residues: 132.1866 Evaluate side-chains 239 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 2.372 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1974 time to fit residues: 9.5958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 0.3980 chunk 165 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 147 optimal weight: 0.8980 chunk 220 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN J 49 HIS K 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 20917 Z= 0.165 Angle : 0.576 12.874 28380 Z= 0.283 Chirality : 0.043 0.315 3541 Planarity : 0.003 0.043 3499 Dihedral : 4.150 23.766 2591 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.16), residues: 2441 helix: 0.56 (0.19), residues: 712 sheet: -0.29 (0.23), residues: 476 loop : -1.29 (0.16), residues: 1253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 266 average time/residue: 0.2920 time to fit residues: 124.6081 Evaluate side-chains 242 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 232 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1855 time to fit residues: 6.4228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 20917 Z= 0.305 Angle : 0.639 10.216 28380 Z= 0.318 Chirality : 0.045 0.308 3541 Planarity : 0.004 0.044 3499 Dihedral : 4.352 29.929 2591 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2441 helix: 0.73 (0.20), residues: 702 sheet: -0.38 (0.23), residues: 484 loop : -1.30 (0.16), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 262 average time/residue: 0.3100 time to fit residues: 131.5054 Evaluate side-chains 237 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1900 time to fit residues: 11.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN H 129 GLN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 20917 Z= 0.195 Angle : 0.595 12.847 28380 Z= 0.292 Chirality : 0.043 0.298 3541 Planarity : 0.003 0.040 3499 Dihedral : 4.222 27.873 2591 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2441 helix: 0.95 (0.20), residues: 705 sheet: -0.36 (0.24), residues: 474 loop : -1.26 (0.16), residues: 1262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 263 average time/residue: 0.2998 time to fit residues: 125.9955 Evaluate side-chains 235 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 218 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2003 time to fit residues: 9.5329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** J 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 20917 Z= 0.329 Angle : 0.674 11.739 28380 Z= 0.333 Chirality : 0.045 0.307 3541 Planarity : 0.004 0.047 3499 Dihedral : 4.438 28.568 2591 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2441 helix: 0.88 (0.20), residues: 710 sheet: -0.52 (0.23), residues: 482 loop : -1.33 (0.16), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 255 average time/residue: 0.2916 time to fit residues: 119.3737 Evaluate side-chains 234 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 2.420 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1845 time to fit residues: 9.9352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 20917 Z= 0.184 Angle : 0.621 12.229 28380 Z= 0.302 Chirality : 0.044 0.348 3541 Planarity : 0.003 0.044 3499 Dihedral : 4.240 25.135 2591 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2441 helix: 1.00 (0.20), residues: 715 sheet: -0.42 (0.24), residues: 446 loop : -1.21 (0.16), residues: 1280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 258 average time/residue: 0.3150 time to fit residues: 128.9328 Evaluate side-chains 234 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1986 time to fit residues: 7.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.0570 chunk 203 optimal weight: 0.0040 chunk 217 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 196 optimal weight: 20.0000 chunk 205 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 overall best weight: 0.7914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN J 64 ASN ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 20917 Z= 0.190 Angle : 0.620 11.991 28380 Z= 0.302 Chirality : 0.044 0.326 3541 Planarity : 0.004 0.109 3499 Dihedral : 4.149 25.255 2591 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2441 helix: 1.11 (0.20), residues: 711 sheet: -0.37 (0.24), residues: 456 loop : -1.14 (0.17), residues: 1274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 239 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 242 average time/residue: 0.3023 time to fit residues: 116.6960 Evaluate side-chains 224 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1856 time to fit residues: 3.6026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 0.0570 chunk 140 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 20917 Z= 0.182 Angle : 0.625 14.155 28380 Z= 0.302 Chirality : 0.044 0.321 3541 Planarity : 0.003 0.045 3499 Dihedral : 4.094 24.839 2591 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2441 helix: 1.20 (0.20), residues: 705 sheet: -0.32 (0.24), residues: 455 loop : -1.11 (0.17), residues: 1281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4882 Ramachandran restraints generated. 2441 Oldfield, 0 Emsley, 2441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 238 average time/residue: 0.2957 time to fit residues: 113.9676 Evaluate side-chains 224 residues out of total 2150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 221 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2183 time to fit residues: 4.3595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 197 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 ASN ** L 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.112367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.080961 restraints weight = 52470.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081081 restraints weight = 33112.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082415 restraints weight = 24960.984| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 20917 Z= 0.203 Angle : 0.628 14.059 28380 Z= 0.306 Chirality : 0.044 0.321 3541 Planarity : 0.003 0.045 3499 Dihedral : 4.087 24.922 2591 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2441 helix: 1.25 (0.20), residues: 705 sheet: -0.37 (0.24), residues: 461 loop : -1.11 (0.17), residues: 1275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.55 seconds wall clock time: 68 minutes 43.80 seconds (4123.80 seconds total)