Starting phenix.real_space_refine on Mon Mar 25 06:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm9_22390/03_2024/7jm9_22390_trim_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 120 5.16 5 C 15360 2.51 5 N 3156 2.21 5 O 3612 1.98 5 H 18876 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 151": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 151": "OE1" <-> "OE2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 151": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 151": "OE1" <-> "OE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 151": "OE1" <-> "OE2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 151": "OE1" <-> "OE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 151": "OE1" <-> "OE2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 151": "OE1" <-> "OE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 151": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 151": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 151": "OE1" <-> "OE2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 151": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41136 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "D" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "E" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "F" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "G" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "I" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "K" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "L" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3158 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 186} Chain breaks: 1 Chain: "A" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "D" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "F" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "G" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "I" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "J" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "K" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 257 Unusual residues: {'MC3': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'MC3:plan-2': 10, 'MC3:plan-1': 10} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 17.82, per 1000 atoms: 0.43 Number of scatterers: 41136 At special positions: 0 Unit cell: (99.297, 99.297, 169.389, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 12 15.00 O 3612 8.00 N 3156 7.00 C 15360 6.00 H 18876 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 33.77 Conformation dependent library (CDL) restraints added in 4.5 seconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 69.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 106 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 153 through 180 Processing helix chain 'A' and resid 206 through 235 Processing helix chain 'B' and resid 5 through 16 Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 106 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 153 through 180 Processing helix chain 'B' and resid 206 through 235 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 41 through 44 No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 74 through 106 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 153 through 180 Processing helix chain 'C' and resid 206 through 235 Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 74 through 106 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 153 through 180 Processing helix chain 'D' and resid 206 through 235 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 74 through 106 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 153 through 180 Processing helix chain 'E' and resid 206 through 235 Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 74 through 106 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 153 through 180 Processing helix chain 'F' and resid 206 through 235 Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 20 through 32 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 106 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 153 through 180 Processing helix chain 'G' and resid 206 through 235 Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 20 through 32 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 74 through 106 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 153 through 180 Processing helix chain 'H' and resid 206 through 235 Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 20 through 32 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 44 No H-bonds generated for 'chain 'I' and resid 41 through 44' Processing helix chain 'I' and resid 61 through 69 Processing helix chain 'I' and resid 74 through 106 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 153 through 180 Processing helix chain 'I' and resid 206 through 235 Processing helix chain 'J' and resid 5 through 16 Processing helix chain 'J' and resid 20 through 32 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 106 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 153 through 180 Processing helix chain 'J' and resid 206 through 235 Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 20 through 32 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 44 No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 74 through 106 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 153 through 180 Processing helix chain 'K' and resid 206 through 235 Processing helix chain 'L' and resid 5 through 16 Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 74 through 106 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 153 through 180 Processing helix chain 'L' and resid 206 through 235 Processing sheet with id= A, first strand: chain 'A' and resid 187 through 190 Processing sheet with id= B, first strand: chain 'B' and resid 187 through 190 Processing sheet with id= C, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= D, first strand: chain 'D' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'E' and resid 187 through 190 Processing sheet with id= F, first strand: chain 'F' and resid 187 through 190 Processing sheet with id= G, first strand: chain 'G' and resid 187 through 190 Processing sheet with id= H, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= I, first strand: chain 'I' and resid 187 through 190 Processing sheet with id= J, first strand: chain 'J' and resid 187 through 190 Processing sheet with id= K, first strand: chain 'K' and resid 187 through 190 Processing sheet with id= L, first strand: chain 'L' and resid 187 through 190 1248 hydrogen bonds defined for protein. 3708 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: 14.32 Time building geometry restraints manager: 34.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.73 - 0.94: 5496 0.94 - 1.16: 13368 1.16 - 1.38: 7402 1.38 - 1.59: 14906 1.59 - 1.81: 180 Bond restraints: 41352 Sorted by residual: bond pdb=" NE2 GLN H 49 " pdb="HE22 GLN H 49 " ideal model delta sigma weight residual 0.860 0.728 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" NE2 GLN B 49 " pdb="HE22 GLN B 49 " ideal model delta sigma weight residual 0.860 0.728 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" NE2 GLN I 49 " pdb="HE22 GLN I 49 " ideal model delta sigma weight residual 0.860 0.728 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" NE2 GLN F 49 " pdb="HE22 GLN F 49 " ideal model delta sigma weight residual 0.860 0.728 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" NE2 GLN E 49 " pdb="HE22 GLN E 49 " ideal model delta sigma weight residual 0.860 0.728 0.132 2.00e-02 2.50e+03 4.36e+01 ... (remaining 41347 not shown) Histogram of bond angle deviations from ideal: 86.44 - 96.23: 24 96.23 - 106.01: 729 106.01 - 115.80: 49686 115.80 - 125.59: 20678 125.59 - 135.38: 1147 Bond angle restraints: 72264 Sorted by residual: angle pdb="HE21 GLN E 49 " pdb=" NE2 GLN E 49 " pdb="HE22 GLN E 49 " ideal model delta sigma weight residual 120.00 86.44 33.56 3.00e+00 1.11e-01 1.25e+02 angle pdb="HE21 GLN D 49 " pdb=" NE2 GLN D 49 " pdb="HE22 GLN D 49 " ideal model delta sigma weight residual 120.00 86.48 33.52 3.00e+00 1.11e-01 1.25e+02 angle pdb="HE21 GLN C 49 " pdb=" NE2 GLN C 49 " pdb="HE22 GLN C 49 " ideal model delta sigma weight residual 120.00 86.54 33.46 3.00e+00 1.11e-01 1.24e+02 angle pdb="HE21 GLN F 49 " pdb=" NE2 GLN F 49 " pdb="HE22 GLN F 49 " ideal model delta sigma weight residual 120.00 86.55 33.45 3.00e+00 1.11e-01 1.24e+02 angle pdb="HE21 GLN G 49 " pdb=" NE2 GLN G 49 " pdb="HE22 GLN G 49 " ideal model delta sigma weight residual 120.00 86.57 33.43 3.00e+00 1.11e-01 1.24e+02 ... (remaining 72259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.91: 19692 26.91 - 53.82: 648 53.82 - 80.73: 192 80.73 - 107.64: 36 107.64 - 134.55: 24 Dihedral angle restraints: 20592 sinusoidal: 11952 harmonic: 8640 Sorted by residual: dihedral pdb=" C2 MC3 C 512 " pdb=" C31 MC3 C 512 " pdb=" O2 MC3 C 512 " pdb=" C32 MC3 C 512 " ideal model delta sinusoidal sigma weight residual 177.42 -48.03 -134.55 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" C2 MC3 D 512 " pdb=" C31 MC3 D 512 " pdb=" O2 MC3 D 512 " pdb=" C32 MC3 D 512 " ideal model delta sinusoidal sigma weight residual 177.42 -48.04 -134.54 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" C2 MC3 A 505 " pdb=" C31 MC3 A 505 " pdb=" O2 MC3 A 505 " pdb=" C32 MC3 A 505 " ideal model delta sinusoidal sigma weight residual 177.42 -48.04 -134.54 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 20589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2982 0.135 - 0.269: 54 0.269 - 0.404: 0 0.404 - 0.538: 0 0.538 - 0.673: 12 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CG LEU D 154 " pdb=" CB LEU D 154 " pdb=" CD1 LEU D 154 " pdb=" CD2 LEU D 154 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CG LEU A 154 " pdb=" CB LEU A 154 " pdb=" CD1 LEU A 154 " pdb=" CD2 LEU A 154 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CG LEU J 154 " pdb=" CB LEU J 154 " pdb=" CD1 LEU J 154 " pdb=" CD2 LEU J 154 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 3045 not shown) Planarity restraints: 5592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 197 " 0.092 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CG ASN B 197 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN B 197 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN B 197 " 0.131 2.00e-02 2.50e+03 pdb="HD21 ASN B 197 " 0.185 2.00e-02 2.50e+03 pdb="HD22 ASN B 197 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 197 " -0.092 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CG ASN H 197 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN H 197 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN H 197 " -0.131 2.00e-02 2.50e+03 pdb="HD21 ASN H 197 " -0.185 2.00e-02 2.50e+03 pdb="HD22 ASN H 197 " 0.270 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 197 " 0.092 2.00e-02 2.50e+03 1.55e-01 3.59e+02 pdb=" CG ASN D 197 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN D 197 " -0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN D 197 " 0.131 2.00e-02 2.50e+03 pdb="HD21 ASN D 197 " 0.185 2.00e-02 2.50e+03 pdb="HD22 ASN D 197 " -0.270 2.00e-02 2.50e+03 ... (remaining 5589 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3788 2.24 - 2.83: 85584 2.83 - 3.42: 102952 3.42 - 4.01: 145412 4.01 - 4.60: 227626 Nonbonded interactions: 565362 Sorted by model distance: nonbonded pdb="HE21 GLN A 81 " pdb=" OE1 GLU A 169 " model vdw 1.654 1.850 nonbonded pdb="HE21 GLN G 81 " pdb=" OE1 GLU G 169 " model vdw 1.654 1.850 nonbonded pdb="HE21 GLN D 81 " pdb=" OE1 GLU D 169 " model vdw 1.654 1.850 nonbonded pdb="HE21 GLN J 81 " pdb=" OE1 GLU J 169 " model vdw 1.654 1.850 nonbonded pdb="HE21 GLN C 81 " pdb=" OE1 GLU C 169 " model vdw 1.654 1.850 ... (remaining 565357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 236 or (resid 501 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or \ name C43 or name C44 or name O11 or name O2 or name O3 or name O31)) or resid 50 \ 4 or (resid 505 and (name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24)) or resid 506 through 508 or (resid 511 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24)) or resid 512 or (resid 513 and (name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or n \ ame C23 or name C24)) or (resid 514 and (name C15 or name C16 or name C17 or nam \ e C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24))) \ ) selection = (chain 'B' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'C' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'D' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'E' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'F' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C42 or \ name C43 or name C44 or name O11 or name O2 or name O3 or name O31)) or resid 50 \ 4 or (resid 505 and (name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C2 \ 3 or name C24)) or resid 506 through 508 or (resid 511 and (name C13 or name C14 \ or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name \ C21 or name C22 or name C23 or name C24)) or resid 512 or (resid 513 and (name \ C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or n \ ame C23 or name C24)) or (resid 514 and (name C15 or name C16 or name C17 or nam \ e C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24))) \ ) selection = (chain 'H' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'I' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'J' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'K' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) selection = (chain 'L' and (resid 2 through 236 or resid 501 or (resid 504 and (name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or resid 505 or (resid 506 an \ d (name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or (resid 507 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or nam \ e C24)) or (resid 508 and (name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or nam \ e C20 or name C21 or name C22 or name C23 or name C24 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42 or name C43 or name C44 or name \ O11 or name O2 or name O3 or name O31)) or resid 511 or (resid 512 and (name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or nam \ e C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or resid 513 \ through 514)) } 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: 3.150 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: 0.650 Extract box with map and model: 15.250 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 128.200 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.009 0.090 22476 Z= 0.555 Angle : 1.465 14.299 29532 Z= 0.600 Chirality : 0.066 0.673 3048 Planarity : 0.005 0.034 3372 Dihedral : 14.056 134.549 9288 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.10 (0.16), residues: 2280 helix: 0.71 (0.11), residues: 1728 sheet: -0.45 (0.29), residues: 204 loop : -2.53 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 45 HIS 0.010 0.002 HIS C 74 PHE 0.019 0.003 PHE F 70 TYR 0.011 0.003 TYR F 66 ARG 0.006 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 304 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 PHE cc_start: 0.7679 (m-10) cc_final: 0.7469 (m-80) outliers start: 12 outliers final: 14 residues processed: 316 average time/residue: 2.0104 time to fit residues: 756.1024 Evaluate side-chains 278 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 264 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 178 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 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 49 GLN B 49 GLN ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 49 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN G 49 GLN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN J 49 GLN K 49 GLN ** K 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN ** L 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 22476 Z= 0.151 Angle : 0.475 4.243 29532 Z= 0.237 Chirality : 0.038 0.124 3048 Planarity : 0.003 0.024 3372 Dihedral : 11.520 102.727 4984 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.04 % Allowed : 12.05 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.17), residues: 2280 helix: 2.62 (0.12), residues: 1728 sheet: -0.36 (0.30), residues: 204 loop : -2.21 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 45 HIS 0.003 0.001 HIS D 99 PHE 0.010 0.001 PHE A 178 TYR 0.012 0.002 TYR G 66 ARG 0.007 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 PHE cc_start: 0.7674 (m-10) cc_final: 0.7457 (m-80) outliers start: 22 outliers final: 16 residues processed: 254 average time/residue: 2.2617 time to fit residues: 673.1190 Evaluate side-chains 225 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 209 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS J 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22476 Z= 0.291 Angle : 0.533 4.446 29532 Z= 0.274 Chirality : 0.041 0.137 3048 Planarity : 0.004 0.054 3372 Dihedral : 12.794 93.287 4980 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.45 % Allowed : 10.12 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.17), residues: 2280 helix: 2.64 (0.12), residues: 1716 sheet: -0.31 (0.30), residues: 204 loop : -2.03 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 193 HIS 0.005 0.001 HIS G 176 PHE 0.017 0.002 PHE I 202 TYR 0.018 0.003 TYR G 66 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 247 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 183 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7448 (ttm-80) REVERT: K 36 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 52 outliers final: 26 residues processed: 287 average time/residue: 2.7018 time to fit residues: 885.3354 Evaluate side-chains 241 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 17 HIS C 176 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 176 HIS G 176 HIS I 176 HIS K 176 HIS L 176 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22476 Z= 0.205 Angle : 0.460 4.207 29532 Z= 0.234 Chirality : 0.038 0.121 3048 Planarity : 0.003 0.023 3372 Dihedral : 10.793 89.918 4980 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.07 % Allowed : 13.37 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 2280 helix: 3.02 (0.12), residues: 1716 sheet: -0.22 (0.31), residues: 204 loop : -2.01 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 193 HIS 0.004 0.001 HIS A 176 PHE 0.013 0.002 PHE A 212 TYR 0.014 0.002 TYR D 66 ARG 0.002 0.000 ARG K 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 149 ARG cc_start: 0.6158 (OUTLIER) cc_final: 0.5521 (pmt-80) REVERT: I 156 ARG cc_start: 0.6609 (tpt170) cc_final: 0.6390 (mmt-90) REVERT: L 149 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5430 (pmt-80) outliers start: 44 outliers final: 29 residues processed: 299 average time/residue: 2.9458 time to fit residues: 995.0615 Evaluate side-chains 293 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 HIS F 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22476 Z= 0.283 Angle : 0.507 4.297 29532 Z= 0.260 Chirality : 0.040 0.123 3048 Planarity : 0.004 0.053 3372 Dihedral : 11.558 89.168 4980 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.45 % Allowed : 15.11 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.17), residues: 2280 helix: 2.84 (0.12), residues: 1716 sheet: -0.26 (0.30), residues: 204 loop : -1.77 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 193 HIS 0.005 0.001 HIS J 176 PHE 0.017 0.002 PHE L 202 TYR 0.017 0.002 TYR D 66 ARG 0.011 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 281 time to evaluate : 3.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5661 (pmt-80) REVERT: B 149 ARG cc_start: 0.6233 (OUTLIER) cc_final: 0.5529 (pmt-80) REVERT: C 149 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5739 (pmt-80) REVERT: E 149 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5572 (pmt-80) REVERT: F 149 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5673 (pmt-80) REVERT: I 149 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5636 (pmt-80) REVERT: L 149 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5573 (pmt-80) outliers start: 52 outliers final: 34 residues processed: 314 average time/residue: 2.9610 time to fit residues: 1050.3243 Evaluate side-chains 314 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS F 15 ASN H 9 ASN J 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22476 Z= 0.186 Angle : 0.454 4.069 29532 Z= 0.230 Chirality : 0.038 0.119 3048 Planarity : 0.003 0.027 3372 Dihedral : 10.325 83.077 4980 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.40 % Allowed : 15.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.17), residues: 2280 helix: 3.09 (0.12), residues: 1716 sheet: -0.17 (0.32), residues: 204 loop : -1.72 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 193 HIS 0.003 0.001 HIS C 161 PHE 0.013 0.001 PHE K 202 TYR 0.014 0.002 TYR D 66 ARG 0.002 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5660 (pmt-80) REVERT: B 149 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5658 (pmt-80) REVERT: C 149 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5729 (pmt-80) REVERT: E 149 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5705 (pmt-80) REVERT: F 149 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5658 (pmt-80) REVERT: I 149 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5646 (pmt-80) REVERT: L 149 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5575 (pmt-80) outliers start: 51 outliers final: 35 residues processed: 320 average time/residue: 3.0933 time to fit residues: 1112.8881 Evaluate side-chains 322 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN G 17 HIS J 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22476 Z= 0.309 Angle : 0.522 4.292 29532 Z= 0.267 Chirality : 0.041 0.124 3048 Planarity : 0.003 0.024 3372 Dihedral : 11.694 87.659 4980 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.31 % Allowed : 15.44 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.17), residues: 2280 helix: 2.80 (0.12), residues: 1716 sheet: -0.20 (0.30), residues: 204 loop : -1.65 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 193 HIS 0.004 0.001 HIS D 161 PHE 0.018 0.002 PHE F 202 TYR 0.019 0.003 TYR D 66 ARG 0.003 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 295 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5721 (pmt-80) REVERT: B 149 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5737 (pmt-80) REVERT: C 149 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.5809 (pmt-80) REVERT: E 149 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5783 (pmt-80) REVERT: F 149 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.5718 (pmt-80) REVERT: I 149 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5649 (pmt-80) REVERT: L 149 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5619 (pmt-80) REVERT: L 156 ARG cc_start: 0.6477 (mmt-90) cc_final: 0.6226 (mmt-90) outliers start: 49 outliers final: 35 residues processed: 326 average time/residue: 2.8597 time to fit residues: 1057.6571 Evaluate side-chains 329 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 287 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 102 MET Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22476 Z= 0.177 Angle : 0.454 4.049 29532 Z= 0.229 Chirality : 0.038 0.118 3048 Planarity : 0.003 0.022 3372 Dihedral : 10.181 81.933 4980 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.21 % Allowed : 15.54 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.17), residues: 2280 helix: 3.11 (0.12), residues: 1716 sheet: -0.08 (0.32), residues: 204 loop : -1.64 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 193 HIS 0.003 0.001 HIS D 161 PHE 0.013 0.001 PHE B 202 TYR 0.013 0.002 TYR D 66 ARG 0.002 0.000 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.6352 (OUTLIER) cc_final: 0.5702 (pmt-80) REVERT: B 149 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5698 (pmt-80) REVERT: B 156 ARG cc_start: 0.6658 (mpt180) cc_final: 0.6323 (mpt90) REVERT: C 149 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5735 (pmt-80) REVERT: E 149 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5718 (pmt-80) REVERT: F 149 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5664 (pmt-80) REVERT: I 149 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5644 (pmt-80) REVERT: L 149 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5583 (pmt-80) REVERT: L 156 ARG cc_start: 0.6444 (mmt-90) cc_final: 0.6195 (mmt-90) outliers start: 47 outliers final: 34 residues processed: 322 average time/residue: 2.9610 time to fit residues: 1083.8799 Evaluate side-chains 332 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 102 MET Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22476 Z= 0.179 Angle : 0.454 5.034 29532 Z= 0.229 Chirality : 0.038 0.118 3048 Planarity : 0.003 0.059 3372 Dihedral : 9.857 80.842 4980 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.17 % Allowed : 15.91 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.17), residues: 2280 helix: 3.18 (0.12), residues: 1716 sheet: -0.09 (0.32), residues: 204 loop : -1.64 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 193 HIS 0.002 0.001 HIS D 161 PHE 0.013 0.001 PHE B 202 TYR 0.013 0.002 TYR D 66 ARG 0.011 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 296 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5695 (pmt-80) REVERT: B 156 ARG cc_start: 0.6659 (mpt180) cc_final: 0.6329 (mpt90) REVERT: C 149 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.5719 (pmt-80) REVERT: E 149 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5668 (pmt-80) REVERT: F 149 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5612 (pmt-80) REVERT: I 149 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5571 (pmt-80) REVERT: L 149 ARG cc_start: 0.6094 (OUTLIER) cc_final: 0.5486 (pmt-80) REVERT: L 156 ARG cc_start: 0.6416 (mmt-90) cc_final: 0.6178 (mmt-90) outliers start: 46 outliers final: 36 residues processed: 327 average time/residue: 2.9249 time to fit residues: 1083.6528 Evaluate side-chains 333 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 291 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 102 MET Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22476 Z= 0.186 Angle : 0.457 4.072 29532 Z= 0.231 Chirality : 0.038 0.118 3048 Planarity : 0.003 0.022 3372 Dihedral : 9.772 80.283 4980 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.93 % Allowed : 16.10 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.17), residues: 2280 helix: 3.17 (0.12), residues: 1716 sheet: -0.10 (0.32), residues: 204 loop : -1.64 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 193 HIS 0.002 0.001 HIS G 161 PHE 0.013 0.001 PHE K 202 TYR 0.013 0.002 TYR D 66 ARG 0.002 0.000 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 295 time to evaluate : 3.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5700 (pmt-80) REVERT: B 156 ARG cc_start: 0.6667 (mpt180) cc_final: 0.6339 (mpt90) REVERT: C 149 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5722 (pmt-80) REVERT: E 149 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.5697 (pmt-80) REVERT: F 149 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5539 (pmt-80) REVERT: I 149 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5532 (pmt-80) REVERT: L 149 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5457 (pmt-80) REVERT: L 156 ARG cc_start: 0.6417 (mmt-90) cc_final: 0.6176 (mmt-90) outliers start: 41 outliers final: 35 residues processed: 325 average time/residue: 3.0166 time to fit residues: 1122.5892 Evaluate side-chains 336 residues out of total 2124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 295 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 149 ARG Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 149 ARG Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 102 MET Chi-restraints excluded: chain L residue 149 ARG Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.164232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117730 restraints weight = 56393.128| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.39 r_work: 0.3189 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22476 Z= 0.121 Angle : 0.417 5.136 29532 Z= 0.208 Chirality : 0.037 0.123 3048 Planarity : 0.002 0.058 3372 Dihedral : 8.610 74.587 4980 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.37 % Allowed : 16.71 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.18), residues: 2280 helix: 3.51 (0.12), residues: 1716 sheet: -0.11 (0.33), residues: 204 loop : -1.71 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP I 193 HIS 0.005 0.000 HIS D 233 PHE 0.009 0.001 PHE B 202 TYR 0.008 0.001 TYR D 66 ARG 0.012 0.000 ARG D 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15115.15 seconds wall clock time: 264 minutes 1.76 seconds (15841.76 seconds total)