Starting phenix.real_space_refine on Sun Mar 17 22:22:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xl8_33274/03_2024/7xl8_33274_trim_updated.pdb" } resolution = 3.0 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= 0.045 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 156 5.16 5 C 11556 2.51 5 N 2508 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F ARG 246": "NH1" <-> "NH2" Residue "F GLU 249": "OE1" <-> "OE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 49": "OE1" <-> "OE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G ARG 246": "NH1" <-> "NH2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H ARG 246": "NH1" <-> "NH2" Residue "H GLU 249": "OE1" <-> "OE2" Residue "H PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 77": "NH1" <-> "NH2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I ARG 246": "NH1" <-> "NH2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 24": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J ARG 246": "NH1" <-> "NH2" Residue "J GLU 249": "OE1" <-> "OE2" Residue "J PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K ARG 246": "NH1" <-> "NH2" Residue "K GLU 249": "OE1" <-> "OE2" Residue "K PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 34": "NH1" <-> "NH2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L ARG 246": "NH1" <-> "NH2" Residue "L GLU 249": "OE1" <-> "OE2" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16920 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "B" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "C" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "D" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "E" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "F" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "G" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "I" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "J" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "K" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "L" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'MC3': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 9.42, per 1000 atoms: 0.56 Number of scatterers: 16920 At special positions: 0 Unit cell: (93.4065, 100.139, 143.897, 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 156 16.00 O 2700 8.00 N 2508 7.00 C 11556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.05 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.05 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.05 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.05 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.05 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.05 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.05 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.05 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.05 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.05 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.05 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.05 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.05 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.05 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.05 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.05 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.05 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.05 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.05 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.05 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.05 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.05 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.05 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.05 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.05 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.05 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.05 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.05 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.05 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.05 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.05 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 Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 3.1 seconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 12 sheets defined 67.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE A 37 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 38 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 40 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.504A pdb=" N SER A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 40 removed outlier: 3.783A pdb=" N ILE B 37 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 38 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 39 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 40 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.504A pdb=" N SER B 97 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 275 removed outlier: 3.625A pdb=" N GLU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE C 37 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 38 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 39 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 40 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 75 through 99 removed outlier: 3.542A pdb=" N CYS C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.504A pdb=" N SER C 97 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE D 37 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL D 38 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 39 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 40 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.504A pdb=" N SER D 97 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE E 37 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL E 38 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA E 39 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE E 40 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 99 removed outlier: 3.540A pdb=" N CYS E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 3.504A pdb=" N SER E 97 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE E 201 " --> pdb=" O ARG E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 275 removed outlier: 3.625A pdb=" N GLU E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE F 37 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL F 38 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA F 39 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 No H-bonds generated for 'chain 'F' and resid 42 through 45' Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 99 removed outlier: 3.542A pdb=" N CYS F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Proline residue: F 89 - end of helix removed outlier: 3.504A pdb=" N SER F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 220 removed outlier: 3.682A pdb=" N ILE F 201 " --> pdb=" O ARG F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE G 37 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL G 38 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA G 39 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 40 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 45 No H-bonds generated for 'chain 'G' and resid 42 through 45' Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS G 87 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR G 88 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.505A pdb=" N SER G 97 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE G 201 " --> pdb=" O ARG G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU G 271 " --> pdb=" O LEU G 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN G 273 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE H 37 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL H 38 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA H 39 " --> pdb=" O LEU H 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE H 40 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 45 No H-bonds generated for 'chain 'H' and resid 42 through 45' Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS H 87 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR H 88 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Proline residue: H 89 - end of helix removed outlier: 3.504A pdb=" N SER H 97 " --> pdb=" O PHE H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE H 201 " --> pdb=" O ARG H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 275 removed outlier: 3.625A pdb=" N GLU H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN H 273 " --> pdb=" O LEU H 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE I 37 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL I 38 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA I 39 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE I 40 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 45 No H-bonds generated for 'chain 'I' and resid 42 through 45' Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 75 through 99 removed outlier: 3.540A pdb=" N CYS I 87 " --> pdb=" O ILE I 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR I 88 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Proline residue: I 89 - end of helix removed outlier: 3.505A pdb=" N SER I 97 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE I 201 " --> pdb=" O ARG I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 275 removed outlier: 3.625A pdb=" N GLU I 271 " --> pdb=" O LEU I 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS I 274 " --> pdb=" O ALA I 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU I 275 " --> pdb=" O GLU I 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE J 37 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL J 38 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA J 39 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE J 40 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 45 No H-bonds generated for 'chain 'J' and resid 42 through 45' Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 75 through 99 removed outlier: 3.540A pdb=" N CYS J 87 " --> pdb=" O ILE J 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR J 88 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Proline residue: J 89 - end of helix removed outlier: 3.504A pdb=" N SER J 97 " --> pdb=" O PHE J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE J 201 " --> pdb=" O ARG J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN J 273 " --> pdb=" O LEU J 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS J 274 " --> pdb=" O ALA J 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU J 275 " --> pdb=" O GLU J 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL K 38 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA K 39 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE K 40 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 45 No H-bonds generated for 'chain 'K' and resid 42 through 45' Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS K 87 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 88 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Proline residue: K 89 - end of helix removed outlier: 3.504A pdb=" N SER K 97 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE K 201 " --> pdb=" O ARG K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 275 removed outlier: 3.625A pdb=" N GLU K 271 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN K 273 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS K 274 " --> pdb=" O ALA K 270 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 275 " --> pdb=" O GLU K 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 40 removed outlier: 3.784A pdb=" N ILE L 37 " --> pdb=" O ARG L 34 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL L 38 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA L 39 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE L 40 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 45 No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 99 removed outlier: 3.541A pdb=" N CYS L 87 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Proline residue: L 89 - end of helix removed outlier: 3.505A pdb=" N SER L 97 " --> pdb=" O PHE L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 220 removed outlier: 3.681A pdb=" N ILE L 201 " --> pdb=" O ARG L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 275 removed outlier: 3.624A pdb=" N GLU L 271 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN L 273 " --> pdb=" O LEU L 269 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS L 274 " --> pdb=" O ALA L 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU L 275 " --> pdb=" O GLU L 271 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 228 through 231 Processing sheet with id= B, first strand: chain 'B' and resid 228 through 231 Processing sheet with id= C, first strand: chain 'C' and resid 228 through 231 Processing sheet with id= D, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= E, first strand: chain 'E' and resid 228 through 231 Processing sheet with id= F, first strand: chain 'F' and resid 228 through 231 Processing sheet with id= G, first strand: chain 'G' and resid 228 through 231 Processing sheet with id= H, first strand: chain 'H' and resid 228 through 231 Processing sheet with id= I, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= J, first strand: chain 'J' and resid 228 through 231 Processing sheet with id= K, first strand: chain 'K' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'L' and resid 228 through 231 912 hydrogen bonds defined for protein. 2268 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: 4.11 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2400 1.31 - 1.44: 4656 1.44 - 1.57: 9960 1.57 - 1.69: 0 1.69 - 1.82: 204 Bond restraints: 17220 Sorted by residual: bond pdb=" C ARG H 34 " pdb=" O ARG H 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.29e+01 bond pdb=" C ARG D 34 " pdb=" O ARG D 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" C ARG E 34 " pdb=" O ARG E 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.27e+01 bond pdb=" C ARG F 34 " pdb=" O ARG F 34 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.15e-02 7.56e+03 2.26e+01 bond pdb=" C ARG L 34 " pdb=" O ARG L 34 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.15e-02 7.56e+03 2.26e+01 ... (remaining 17215 not shown) Histogram of bond angle deviations from ideal: 101.13 - 107.68: 660 107.68 - 114.22: 9852 114.22 - 120.77: 7528 120.77 - 127.31: 4772 127.31 - 133.86: 132 Bond angle restraints: 22944 Sorted by residual: angle pdb=" N ILE J 37 " pdb=" CA ILE J 37 " pdb=" C ILE J 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.92e+01 angle pdb=" N ILE C 37 " pdb=" CA ILE C 37 " pdb=" C ILE C 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.92e+01 angle pdb=" N ILE H 37 " pdb=" CA ILE H 37 " pdb=" C ILE H 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ILE F 37 " pdb=" CA ILE F 37 " pdb=" C ILE F 37 " ideal model delta sigma weight residual 111.00 104.18 6.82 1.09e+00 8.42e-01 3.91e+01 angle pdb=" N ILE K 37 " pdb=" CA ILE K 37 " pdb=" C ILE K 37 " ideal model delta sigma weight residual 111.00 104.20 6.80 1.09e+00 8.42e-01 3.90e+01 ... (remaining 22939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8456 17.14 - 34.29: 1247 34.29 - 51.43: 533 51.43 - 68.58: 144 68.58 - 85.72: 24 Dihedral angle restraints: 10404 sinusoidal: 4656 harmonic: 5748 Sorted by residual: dihedral pdb=" N LEU E 36 " pdb=" C LEU E 36 " pdb=" CA LEU E 36 " pdb=" CB LEU E 36 " ideal model delta harmonic sigma weight residual 122.80 135.63 -12.83 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LEU J 36 " pdb=" C LEU J 36 " pdb=" CA LEU J 36 " pdb=" CB LEU J 36 " ideal model delta harmonic sigma weight residual 122.80 135.62 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" N LEU D 36 " pdb=" C LEU D 36 " pdb=" CA LEU D 36 " pdb=" CB LEU D 36 " ideal model delta harmonic sigma weight residual 122.80 135.61 -12.81 0 2.50e+00 1.60e-01 2.63e+01 ... (remaining 10401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2171 0.089 - 0.178: 337 0.178 - 0.267: 36 0.267 - 0.356: 12 0.356 - 0.446: 12 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA LEU J 36 " pdb=" N LEU J 36 " pdb=" C LEU J 36 " pdb=" CB LEU J 36 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA LEU E 36 " pdb=" N LEU E 36 " pdb=" C LEU E 36 " pdb=" CB LEU E 36 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CA LEU D 36 " pdb=" N LEU D 36 " pdb=" C LEU D 36 " pdb=" CB LEU D 36 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2565 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 198 " 0.021 2.00e-02 2.50e+03 2.19e-02 8.43e+00 pdb=" CG PHE G 198 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE G 198 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE G 198 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE G 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 198 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G 198 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 198 " -0.021 2.00e-02 2.50e+03 2.19e-02 8.37e+00 pdb=" CG PHE F 198 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE F 198 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 198 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 198 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 198 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 198 " 0.022 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE L 198 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE L 198 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE L 198 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE L 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE L 198 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE L 198 " 0.001 2.00e-02 2.50e+03 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3586 2.78 - 3.31: 14894 3.31 - 3.84: 26280 3.84 - 4.37: 30395 4.37 - 4.90: 53904 Nonbonded interactions: 129059 Sorted by model distance: nonbonded pdb=" O ILE B 22 " pdb=" CG1 ILE B 25 " model vdw 2.249 3.440 nonbonded pdb=" O ILE E 22 " pdb=" CG1 ILE E 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE F 22 " pdb=" CG1 ILE F 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE C 22 " pdb=" CG1 ILE C 25 " model vdw 2.250 3.440 nonbonded pdb=" O ILE J 22 " pdb=" CG1 ILE J 25 " model vdw 2.250 3.440 ... (remaining 129054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.010 Extract box with map and model: 10.690 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 44.770 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.160 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:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 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 : 0.010 0.092 17220 Z= 0.645 Angle : 1.308 11.572 22944 Z= 0.698 Chirality : 0.073 0.446 2568 Planarity : 0.007 0.052 2712 Dihedral : 19.595 85.719 6600 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.35 % Allowed : 25.68 % Favored : 72.97 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 16.67 % 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: -1.48 (0.17), residues: 1908 helix: -1.03 (0.12), residues: 1236 sheet: 0.54 (0.41), residues: 144 loop : -0.78 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B 79 HIS 0.011 0.004 HIS C 274 PHE 0.051 0.003 PHE G 198 TYR 0.011 0.003 TYR B 67 ARG 0.011 0.002 ARG J 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 291 time to evaluate : 1.864 Fit side-chains REVERT: A 21 MET cc_start: 0.4421 (mpm) cc_final: 0.3764 (pmm) REVERT: A 201 ILE cc_start: 0.8281 (mm) cc_final: 0.8036 (tt) REVERT: B 21 MET cc_start: 0.4785 (mpm) cc_final: 0.4253 (pmm) REVERT: C 21 MET cc_start: 0.4834 (mpm) cc_final: 0.3982 (pmm) REVERT: C 69 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7167 (tpp-160) REVERT: C 201 ILE cc_start: 0.8297 (mm) cc_final: 0.8022 (tt) REVERT: D 21 MET cc_start: 0.4631 (mpm) cc_final: 0.4089 (pmm) REVERT: E 21 MET cc_start: 0.4481 (mpm) cc_final: 0.4134 (pmm) REVERT: F 21 MET cc_start: 0.4498 (mpm) cc_final: 0.3902 (pmm) REVERT: G 21 MET cc_start: 0.4594 (mpm) cc_final: 0.4018 (pmm) REVERT: G 69 ARG cc_start: 0.7479 (tpt170) cc_final: 0.7248 (tpp-160) REVERT: H 21 MET cc_start: 0.4341 (mpm) cc_final: 0.3759 (pmm) REVERT: I 21 MET cc_start: 0.4375 (mpm) cc_final: 0.3774 (pmm) REVERT: J 21 MET cc_start: 0.4845 (mpm) cc_final: 0.4001 (pmm) REVERT: J 69 ARG cc_start: 0.7416 (tpt170) cc_final: 0.7142 (tpp-160) REVERT: J 201 ILE cc_start: 0.8287 (mm) cc_final: 0.8009 (tt) REVERT: K 21 MET cc_start: 0.4642 (mpm) cc_final: 0.3981 (pmm) REVERT: L 21 MET cc_start: 0.4873 (mpm) cc_final: 0.4333 (pmm) outliers start: 24 outliers final: 19 residues processed: 314 average time/residue: 1.1024 time to fit residues: 390.0016 Evaluate side-chains 257 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 238 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 34 ARG Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 40 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 174 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 274 HIS C 273 ASN C 274 HIS H 273 ASN H 274 HIS I 274 HIS J 273 ASN J 274 HIS K 273 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17220 Z= 0.177 Angle : 0.583 8.672 22944 Z= 0.311 Chirality : 0.041 0.129 2568 Planarity : 0.006 0.036 2712 Dihedral : 15.000 59.822 3134 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.15 % Allowed : 24.04 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.18), residues: 1908 helix: 0.66 (0.14), residues: 1260 sheet: 0.57 (0.35), residues: 144 loop : -0.51 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.005 0.002 HIS D 274 PHE 0.020 0.001 PHE A 33 TYR 0.008 0.001 TYR B 218 ARG 0.002 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 248 time to evaluate : 1.952 Fit side-chains REVERT: A 21 MET cc_start: 0.4271 (mpm) cc_final: 0.3681 (pmm) REVERT: B 21 MET cc_start: 0.4760 (mpm) cc_final: 0.4460 (pmm) REVERT: C 21 MET cc_start: 0.4690 (mpm) cc_final: 0.4111 (pmm) REVERT: D 21 MET cc_start: 0.4399 (mpm) cc_final: 0.3966 (pmm) REVERT: E 21 MET cc_start: 0.4692 (mpm) cc_final: 0.4409 (pmm) REVERT: E 69 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7675 (tpp-160) REVERT: F 21 MET cc_start: 0.4355 (mpm) cc_final: 0.3960 (pmm) REVERT: F 69 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6766 (tpm-80) REVERT: G 21 MET cc_start: 0.4338 (mpm) cc_final: 0.3971 (pmm) REVERT: H 21 MET cc_start: 0.4317 (mpm) cc_final: 0.3767 (pmm) REVERT: I 21 MET cc_start: 0.4335 (mpm) cc_final: 0.3808 (pmm) REVERT: I 77 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.5973 (mpp-170) REVERT: J 21 MET cc_start: 0.4688 (mpm) cc_final: 0.4098 (pmm) REVERT: K 21 MET cc_start: 0.4559 (mpm) cc_final: 0.4085 (pmm) REVERT: L 21 MET cc_start: 0.4760 (mpm) cc_final: 0.4353 (pmm) outliers start: 56 outliers final: 11 residues processed: 284 average time/residue: 1.0797 time to fit residues: 346.4109 Evaluate side-chains 247 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS D 273 ASN E 273 ASN L 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17220 Z= 0.216 Angle : 0.577 9.438 22944 Z= 0.303 Chirality : 0.042 0.138 2568 Planarity : 0.005 0.035 2712 Dihedral : 12.610 59.677 3074 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.83 % Allowed : 24.61 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.53 (0.18), residues: 1908 helix: 0.87 (0.14), residues: 1260 sheet: 0.61 (0.35), residues: 144 loop : -0.87 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS J 99 PHE 0.019 0.001 PHE A 33 TYR 0.009 0.001 TYR B 218 ARG 0.003 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 1.832 Fit side-chains REVERT: A 21 MET cc_start: 0.4091 (mpm) cc_final: 0.3479 (pmm) REVERT: A 220 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7018 (tt) REVERT: B 21 MET cc_start: 0.4581 (mpm) cc_final: 0.4259 (pmm) REVERT: B 253 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: C 21 MET cc_start: 0.4451 (mpm) cc_final: 0.3864 (pmm) REVERT: C 220 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6858 (tt) REVERT: D 21 MET cc_start: 0.4270 (mpm) cc_final: 0.3946 (pmm) REVERT: D 220 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.6977 (tt) REVERT: E 253 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: F 21 MET cc_start: 0.4460 (mpm) cc_final: 0.4083 (pmm) REVERT: F 220 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7099 (tt) REVERT: G 21 MET cc_start: 0.4440 (mpm) cc_final: 0.4018 (pmm) REVERT: H 21 MET cc_start: 0.3982 (mpm) cc_final: 0.3487 (pmm) REVERT: H 220 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7011 (tt) REVERT: I 21 MET cc_start: 0.4182 (mpm) cc_final: 0.3638 (pmm) REVERT: I 77 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6278 (mpp-170) REVERT: I 253 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: J 21 MET cc_start: 0.4460 (mpm) cc_final: 0.3853 (pmm) REVERT: J 220 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6844 (tt) REVERT: J 253 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: K 21 MET cc_start: 0.4313 (mpm) cc_final: 0.3908 (pmm) REVERT: K 220 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7048 (tt) REVERT: L 253 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6452 (m-80) outliers start: 68 outliers final: 10 residues processed: 253 average time/residue: 0.9673 time to fit residues: 281.9920 Evaluate side-chains 203 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN F 273 ASN F 274 HIS G 273 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17220 Z= 0.159 Angle : 0.522 8.182 22944 Z= 0.272 Chirality : 0.040 0.123 2568 Planarity : 0.005 0.034 2712 Dihedral : 10.969 58.912 3072 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.94 % Allowed : 27.42 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.02 (0.18), residues: 1908 helix: 1.28 (0.14), residues: 1260 sheet: 0.82 (0.34), residues: 144 loop : -0.77 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.003 0.001 HIS F 99 PHE 0.021 0.001 PHE H 33 TYR 0.008 0.001 TYR B 218 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 210 time to evaluate : 1.686 Fit side-chains REVERT: A 21 MET cc_start: 0.3822 (mpm) cc_final: 0.3236 (pmm) REVERT: A 220 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6855 (tt) REVERT: B 21 MET cc_start: 0.4435 (mpm) cc_final: 0.4211 (pmm) REVERT: C 21 MET cc_start: 0.4286 (mpm) cc_final: 0.3763 (pmm) REVERT: C 220 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6653 (tt) REVERT: D 21 MET cc_start: 0.4201 (mpm) cc_final: 0.3873 (pmm) REVERT: D 220 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6860 (tt) REVERT: E 253 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: F 21 MET cc_start: 0.4290 (mpm) cc_final: 0.3992 (pmm) REVERT: F 69 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6616 (tpm-80) REVERT: G 21 MET cc_start: 0.4346 (mpm) cc_final: 0.3860 (pmm) REVERT: H 21 MET cc_start: 0.4052 (mpm) cc_final: 0.3445 (pmm) REVERT: H 220 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6854 (tt) REVERT: I 21 MET cc_start: 0.4091 (mpm) cc_final: 0.3697 (pmm) REVERT: I 77 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6267 (mpp-170) REVERT: I 253 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: J 21 MET cc_start: 0.4343 (mpm) cc_final: 0.3727 (pmm) REVERT: J 69 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6642 (tpm-80) REVERT: J 220 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6654 (tt) REVERT: K 21 MET cc_start: 0.4192 (mpm) cc_final: 0.3804 (pmm) REVERT: K 220 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6850 (tt) REVERT: L 253 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6448 (m-80) outliers start: 70 outliers final: 12 residues processed: 264 average time/residue: 0.8451 time to fit residues: 258.9864 Evaluate side-chains 214 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 253 PHE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17220 Z= 0.219 Angle : 0.575 9.486 22944 Z= 0.294 Chirality : 0.042 0.129 2568 Planarity : 0.005 0.033 2712 Dihedral : 11.015 59.924 3072 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.01 % Allowed : 28.43 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.87 (0.18), residues: 1908 helix: 1.10 (0.14), residues: 1272 sheet: 0.86 (0.36), residues: 144 loop : -0.72 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 79 HIS 0.004 0.001 HIS L 274 PHE 0.021 0.001 PHE H 33 TYR 0.009 0.001 TYR F 67 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 181 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3858 (mpm) cc_final: 0.3296 (pmm) REVERT: A 220 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6929 (tt) REVERT: B 253 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: C 21 MET cc_start: 0.3970 (mpm) cc_final: 0.3565 (pmm) REVERT: C 69 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6571 (tpm-80) REVERT: C 220 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6622 (tt) REVERT: C 253 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6621 (m-80) REVERT: D 21 MET cc_start: 0.4096 (mpm) cc_final: 0.3737 (pmm) REVERT: D 220 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6913 (tt) REVERT: F 21 MET cc_start: 0.4238 (mpm) cc_final: 0.3863 (pmm) REVERT: F 69 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6617 (tpm-80) REVERT: F 77 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6923 (mpp-170) REVERT: G 21 MET cc_start: 0.4302 (mpm) cc_final: 0.3807 (pmm) REVERT: G 69 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6537 (tpm-80) REVERT: G 77 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6904 (mpp-170) REVERT: H 21 MET cc_start: 0.3921 (mpm) cc_final: 0.3373 (pmm) REVERT: H 220 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6919 (tt) REVERT: I 21 MET cc_start: 0.4083 (mpm) cc_final: 0.3668 (pmm) REVERT: I 77 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6312 (mpp-170) REVERT: J 21 MET cc_start: 0.4142 (mpm) cc_final: 0.3671 (pmm) REVERT: J 220 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.6627 (tt) REVERT: K 21 MET cc_start: 0.4197 (mpm) cc_final: 0.3756 (pmm) REVERT: K 220 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6927 (tt) REVERT: L 253 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6389 (m-80) outliers start: 89 outliers final: 24 residues processed: 256 average time/residue: 0.9847 time to fit residues: 289.3283 Evaluate side-chains 218 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 253 PHE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17220 Z= 0.178 Angle : 0.554 8.436 22944 Z= 0.285 Chirality : 0.041 0.126 2568 Planarity : 0.005 0.032 2712 Dihedral : 10.319 59.878 3072 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.66 % Allowed : 30.12 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.07 (0.18), residues: 1908 helix: 1.23 (0.14), residues: 1272 sheet: 1.10 (0.38), residues: 144 loop : -0.63 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 79 HIS 0.004 0.001 HIS L 274 PHE 0.022 0.001 PHE H 33 TYR 0.008 0.001 TYR C 67 ARG 0.002 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3873 (mpm) cc_final: 0.3424 (pmm) REVERT: A 22 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5851 (pp) REVERT: A 220 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6957 (tt) REVERT: C 21 MET cc_start: 0.3960 (mpm) cc_final: 0.3562 (pmm) REVERT: C 69 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6587 (tpm-80) REVERT: C 220 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6750 (tt) REVERT: D 21 MET cc_start: 0.3999 (mpm) cc_final: 0.3605 (pmm) REVERT: D 22 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5732 (pp) REVERT: D 220 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6880 (tt) REVERT: F 21 MET cc_start: 0.4294 (mpm) cc_final: 0.3793 (pmm) REVERT: F 69 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6592 (tpm-80) REVERT: F 77 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6992 (mpp-170) REVERT: G 21 MET cc_start: 0.4125 (mpm) cc_final: 0.3668 (pmm) REVERT: G 69 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6548 (tpm-80) REVERT: G 77 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6956 (mpp-170) REVERT: H 21 MET cc_start: 0.3885 (mpm) cc_final: 0.3388 (pmm) REVERT: H 22 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5836 (pp) REVERT: H 220 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6936 (tt) REVERT: I 21 MET cc_start: 0.4125 (mpm) cc_final: 0.3731 (pmm) REVERT: I 77 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6360 (mpp-170) REVERT: J 21 MET cc_start: 0.4141 (mpm) cc_final: 0.3670 (pmm) REVERT: J 69 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6581 (tpm-80) REVERT: J 220 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6797 (tt) REVERT: K 21 MET cc_start: 0.4134 (mpm) cc_final: 0.3772 (pmm) REVERT: K 220 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.6930 (tt) REVERT: K 254 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7032 (tp) REVERT: K 274 HIS cc_start: 0.4999 (OUTLIER) cc_final: 0.4485 (m-70) REVERT: L 253 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6443 (m-80) outliers start: 65 outliers final: 19 residues processed: 243 average time/residue: 0.9722 time to fit residues: 270.5001 Evaluate side-chains 221 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 183 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 HIS ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17220 Z= 0.199 Angle : 0.577 9.399 22944 Z= 0.294 Chirality : 0.042 0.127 2568 Planarity : 0.005 0.032 2712 Dihedral : 10.181 59.885 3072 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.94 % Allowed : 30.12 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.05 (0.18), residues: 1908 helix: 1.21 (0.15), residues: 1272 sheet: 1.17 (0.39), residues: 144 loop : -0.66 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 79 HIS 0.004 0.001 HIS L 274 PHE 0.023 0.001 PHE H 33 TYR 0.010 0.001 TYR C 67 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 175 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3791 (mpm) cc_final: 0.3412 (pmm) REVERT: A 22 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5914 (pp) REVERT: A 25 ILE cc_start: 0.5372 (OUTLIER) cc_final: 0.4947 (tp) REVERT: A 220 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6933 (tt) REVERT: B 21 MET cc_start: 0.4746 (pmm) cc_final: 0.4540 (pmm) REVERT: C 21 MET cc_start: 0.4055 (mpm) cc_final: 0.3653 (pmm) REVERT: C 69 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6585 (tpm-80) REVERT: C 220 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6751 (tt) REVERT: D 21 MET cc_start: 0.3757 (mpm) cc_final: 0.3340 (pmm) REVERT: D 22 ILE cc_start: 0.5983 (OUTLIER) cc_final: 0.5659 (pp) REVERT: D 220 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6913 (tt) REVERT: F 21 MET cc_start: 0.3945 (mpm) cc_final: 0.3535 (pmm) REVERT: F 22 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5903 (pp) REVERT: F 69 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6607 (tpm-80) REVERT: F 77 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6972 (mpp-170) REVERT: F 86 VAL cc_start: 0.7611 (m) cc_final: 0.7399 (t) REVERT: G 21 MET cc_start: 0.3968 (mpm) cc_final: 0.3514 (pmm) REVERT: G 22 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5846 (pp) REVERT: G 69 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6561 (tpm-80) REVERT: G 77 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6881 (mpp-170) REVERT: H 21 MET cc_start: 0.3808 (mpm) cc_final: 0.3364 (pmm) REVERT: H 22 ILE cc_start: 0.6141 (OUTLIER) cc_final: 0.5857 (pp) REVERT: H 220 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6952 (tt) REVERT: I 21 MET cc_start: 0.4094 (mpm) cc_final: 0.3681 (pmm) REVERT: I 77 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6414 (mpp-170) REVERT: J 21 MET cc_start: 0.4168 (mpm) cc_final: 0.3693 (pmm) REVERT: J 69 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6613 (tpm-80) REVERT: J 220 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6760 (tt) REVERT: K 21 MET cc_start: 0.4011 (mpm) cc_final: 0.3484 (pmm) REVERT: K 22 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5680 (pp) REVERT: K 220 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.6925 (tt) REVERT: K 254 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7129 (tp) REVERT: K 274 HIS cc_start: 0.5113 (OUTLIER) cc_final: 0.4560 (m-70) REVERT: L 253 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6444 (m-80) outliers start: 70 outliers final: 22 residues processed: 232 average time/residue: 1.0100 time to fit residues: 266.5905 Evaluate side-chains 213 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 168 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.004 0.045 17220 Z= 0.246 Angle : 0.606 9.208 22944 Z= 0.310 Chirality : 0.043 0.132 2568 Planarity : 0.005 0.033 2712 Dihedral : 10.272 59.936 3072 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.66 % Allowed : 30.29 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.92 (0.18), residues: 1908 helix: 1.09 (0.14), residues: 1272 sheet: 1.10 (0.38), residues: 144 loop : -0.62 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 79 HIS 0.005 0.002 HIS B 274 PHE 0.024 0.002 PHE H 33 TYR 0.012 0.002 TYR G 67 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 162 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3670 (mpm) cc_final: 0.3330 (pmm) REVERT: A 22 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5941 (pp) REVERT: A 220 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7023 (tt) REVERT: C 21 MET cc_start: 0.4025 (mpm) cc_final: 0.3604 (pmm) REVERT: C 69 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6575 (tpm-80) REVERT: C 220 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6694 (tt) REVERT: D 21 MET cc_start: 0.3778 (mpm) cc_final: 0.3289 (pmm) REVERT: D 220 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.6995 (tt) REVERT: F 21 MET cc_start: 0.3923 (mpm) cc_final: 0.3541 (pmm) REVERT: F 22 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5949 (pp) REVERT: F 69 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6612 (tpm-80) REVERT: F 77 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6996 (mpp-170) REVERT: F 86 VAL cc_start: 0.7603 (m) cc_final: 0.7380 (t) REVERT: G 21 MET cc_start: 0.4056 (mpm) cc_final: 0.3597 (pmm) REVERT: G 22 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5903 (pp) REVERT: G 69 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6550 (tpm-80) REVERT: G 77 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6930 (mpp-170) REVERT: G 86 VAL cc_start: 0.7638 (m) cc_final: 0.7410 (t) REVERT: G 253 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: H 21 MET cc_start: 0.3658 (mpm) cc_final: 0.3274 (pmm) REVERT: H 22 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5859 (pp) REVERT: H 220 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7057 (tt) REVERT: I 21 MET cc_start: 0.4128 (mpm) cc_final: 0.3738 (pmm) REVERT: I 77 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6339 (mpp-170) REVERT: J 21 MET cc_start: 0.4000 (mpm) cc_final: 0.3586 (pmm) REVERT: J 69 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6614 (tpm-80) REVERT: J 220 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6705 (tt) REVERT: K 21 MET cc_start: 0.3782 (mpm) cc_final: 0.3298 (pmm) REVERT: K 22 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5733 (pp) REVERT: K 220 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7042 (tt) REVERT: K 254 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7246 (tp) REVERT: K 274 HIS cc_start: 0.5026 (OUTLIER) cc_final: 0.4460 (m-70) REVERT: L 253 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6430 (m-80) outliers start: 65 outliers final: 27 residues processed: 215 average time/residue: 1.1252 time to fit residues: 273.6259 Evaluate side-chains 207 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 158 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.0050 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17220 Z= 0.176 Angle : 0.559 8.859 22944 Z= 0.285 Chirality : 0.041 0.126 2568 Planarity : 0.005 0.032 2712 Dihedral : 9.531 59.547 3072 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.27 % Allowed : 30.63 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.17 (0.18), residues: 1908 helix: 1.28 (0.15), residues: 1272 sheet: 1.22 (0.39), residues: 144 loop : -0.56 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.003 0.001 HIS L 274 PHE 0.025 0.001 PHE H 33 TYR 0.011 0.001 TYR F 67 ARG 0.002 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3680 (mpm) cc_final: 0.3351 (pmm) REVERT: A 22 ILE cc_start: 0.6290 (OUTLIER) cc_final: 0.5941 (pp) REVERT: A 25 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5088 (tp) REVERT: A 220 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.6972 (tt) REVERT: C 21 MET cc_start: 0.4105 (mpm) cc_final: 0.3711 (pmm) REVERT: C 25 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.5154 (tp) REVERT: C 69 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7311 (tpm170) REVERT: C 220 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6723 (tt) REVERT: D 21 MET cc_start: 0.3742 (mpm) cc_final: 0.3271 (pmm) REVERT: D 22 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5643 (pp) REVERT: D 25 ILE cc_start: 0.5432 (OUTLIER) cc_final: 0.5031 (tp) REVERT: D 220 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7007 (tt) REVERT: F 21 MET cc_start: 0.3963 (mpm) cc_final: 0.3624 (pmm) REVERT: F 25 ILE cc_start: 0.5624 (OUTLIER) cc_final: 0.5248 (tp) REVERT: F 69 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7314 (tpm170) REVERT: F 77 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7008 (mpp-170) REVERT: F 86 VAL cc_start: 0.7574 (m) cc_final: 0.7349 (t) REVERT: G 21 MET cc_start: 0.3990 (mpm) cc_final: 0.3549 (pmm) REVERT: G 25 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5189 (tp) REVERT: G 69 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7342 (tpm170) REVERT: G 77 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6945 (mpp-170) REVERT: G 86 VAL cc_start: 0.7646 (m) cc_final: 0.7408 (t) REVERT: H 21 MET cc_start: 0.3646 (mpm) cc_final: 0.3273 (pmm) REVERT: H 22 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5824 (pp) REVERT: H 220 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7000 (tt) REVERT: I 21 MET cc_start: 0.4018 (mpm) cc_final: 0.3659 (pmm) REVERT: I 77 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6389 (mpp-170) REVERT: J 21 MET cc_start: 0.4073 (mpm) cc_final: 0.3637 (pmm) REVERT: J 25 ILE cc_start: 0.5478 (OUTLIER) cc_final: 0.5076 (tp) REVERT: J 69 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7307 (tpm170) REVERT: J 220 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6734 (tt) REVERT: K 21 MET cc_start: 0.3834 (mpm) cc_final: 0.3350 (pmm) REVERT: K 22 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5688 (pp) REVERT: K 220 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.6976 (tt) REVERT: K 254 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7036 (tp) REVERT: K 274 HIS cc_start: 0.5002 (OUTLIER) cc_final: 0.4450 (m-70) REVERT: L 253 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6454 (m-80) outliers start: 58 outliers final: 20 residues processed: 235 average time/residue: 1.0437 time to fit residues: 279.2026 Evaluate side-chains 222 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 176 optimal weight: 0.0040 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17220 Z= 0.173 Angle : 0.561 9.660 22944 Z= 0.286 Chirality : 0.041 0.125 2568 Planarity : 0.005 0.032 2712 Dihedral : 9.285 59.810 3072 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.15 % Allowed : 31.36 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.28 (0.19), residues: 1908 helix: 1.36 (0.15), residues: 1272 sheet: 1.35 (0.40), residues: 144 loop : -0.55 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 79 HIS 0.003 0.001 HIS L 274 PHE 0.025 0.001 PHE H 33 TYR 0.019 0.001 TYR G 67 ARG 0.002 0.000 ARG H 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 189 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.3626 (mpm) cc_final: 0.3363 (pmm) REVERT: A 22 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5906 (pp) REVERT: A 25 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5118 (tp) REVERT: A 220 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.6980 (tt) REVERT: B 25 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5257 (tp) REVERT: B 36 LEU cc_start: 0.7097 (pp) cc_final: 0.6851 (mp) REVERT: C 21 MET cc_start: 0.3836 (mpm) cc_final: 0.3583 (pmm) REVERT: C 25 ILE cc_start: 0.5483 (OUTLIER) cc_final: 0.5089 (tp) REVERT: C 49 GLU cc_start: 0.8180 (pt0) cc_final: 0.7935 (pt0) REVERT: C 69 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7350 (tpm170) REVERT: C 86 VAL cc_start: 0.7647 (m) cc_final: 0.7386 (t) REVERT: C 220 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.6791 (tt) REVERT: D 21 MET cc_start: 0.3719 (mpm) cc_final: 0.3264 (pmm) REVERT: D 22 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5619 (pp) REVERT: D 25 ILE cc_start: 0.5445 (OUTLIER) cc_final: 0.5054 (tp) REVERT: D 220 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.6977 (tt) REVERT: E 25 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5143 (tp) REVERT: F 21 MET cc_start: 0.4204 (mpm) cc_final: 0.3761 (pmm) REVERT: F 25 ILE cc_start: 0.5559 (OUTLIER) cc_final: 0.5187 (tp) REVERT: F 69 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7346 (tpm170) REVERT: F 77 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7064 (mpp-170) REVERT: F 86 VAL cc_start: 0.7532 (m) cc_final: 0.7313 (t) REVERT: G 21 MET cc_start: 0.4174 (mpm) cc_final: 0.3711 (pmm) REVERT: G 25 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5127 (tp) REVERT: G 77 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7000 (mpp-170) REVERT: G 86 VAL cc_start: 0.7631 (m) cc_final: 0.7385 (t) REVERT: H 21 MET cc_start: 0.3529 (mpm) cc_final: 0.3217 (pmm) REVERT: H 22 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5835 (pp) REVERT: H 25 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5073 (tp) REVERT: H 220 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.6969 (tt) REVERT: I 21 MET cc_start: 0.3958 (mpm) cc_final: 0.3478 (pmm) REVERT: I 25 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5150 (tp) REVERT: I 77 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6477 (mpp-170) REVERT: J 21 MET cc_start: 0.3760 (mpm) cc_final: 0.3513 (pmm) REVERT: J 25 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.5087 (tp) REVERT: J 49 GLU cc_start: 0.8183 (pt0) cc_final: 0.7940 (pt0) REVERT: J 69 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7347 (tpm170) REVERT: J 86 VAL cc_start: 0.7648 (m) cc_final: 0.7373 (t) REVERT: J 220 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6798 (tt) REVERT: K 21 MET cc_start: 0.3778 (mpm) cc_final: 0.3308 (pmm) REVERT: K 22 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5697 (pp) REVERT: K 25 ILE cc_start: 0.5427 (OUTLIER) cc_final: 0.5032 (tp) REVERT: K 220 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.6980 (tt) REVERT: K 254 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7042 (tp) REVERT: K 274 HIS cc_start: 0.5038 (OUTLIER) cc_final: 0.4439 (m-70) REVERT: L 25 ILE cc_start: 0.5612 (OUTLIER) cc_final: 0.5206 (tp) REVERT: L 253 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6449 (m-80) outliers start: 56 outliers final: 11 residues processed: 234 average time/residue: 1.0510 time to fit residues: 279.4201 Evaluate side-chains 226 residues out of total 1776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 69 ARG Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 69 ARG Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 274 HIS Chi-restraints excluded: chain L residue 25 ILE Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 253 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.207909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168816 restraints weight = 15579.098| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.31 r_work: 0.3614 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17220 Z= 0.142 Angle : 0.531 9.507 22944 Z= 0.270 Chirality : 0.039 0.122 2568 Planarity : 0.004 0.033 2712 Dihedral : 8.665 59.501 3072 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.76 % Allowed : 31.93 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.50 (0.19), residues: 1908 helix: 1.60 (0.15), residues: 1260 sheet: 1.55 (0.41), residues: 144 loop : -0.68 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 79 HIS 0.003 0.001 HIS B 274 PHE 0.027 0.001 PHE A 33 TYR 0.018 0.001 TYR C 67 ARG 0.002 0.000 ARG H 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.44 seconds wall clock time: 97 minutes 13.91 seconds (5833.91 seconds total)